diff --git a/analysis_scripts/run_diamond.sh b/analysis_scripts/run_diamond.sh new file mode 100755 index 0000000..27e37d3 --- /dev/null +++ b/analysis_scripts/run_diamond.sh @@ -0,0 +1,18 @@ +#!/bin/bash + +basedir=${PWD} +species=$1 +faa=$2 + +echo ${basedir} +echo $species +echo ${faa} +./../diamond makedb --in ${faa} -d ${basedir}/${species}/diamond_refseq + +mkdir -p ${basedir}/${species}/Comparison/GFs/diamond +for x in $(ls ${basedir}/${species}/Comparison/GFs/fasta) +do +echo $x +./../diamond blastx -d ${basedir}/${species}/diamond_refseq -q ${basedir}/${species}/Comparison/GFs/fasta/$x -o ${basedir}/${species}/Comparison/GFs/diamond/$x.tsv; +done + diff --git a/analysis_scripts/run_ete3.sh b/analysis_scripts/run_ete3.sh new file mode 100755 index 0000000..e4189df --- /dev/null +++ b/analysis_scripts/run_ete3.sh @@ -0,0 +1,14 @@ +#!/bin/bash +basedir=${PWD} +for sp in synth_myco synth_ecoli synth_paeru; do + for frag in 0.5 0.8 1; do + species=${sp}/${frag} + echo ${species} + #conda activate ete3 + ete3 compare -t ${basedir}/${species}/Comparison/GFs/CG/msa_delos/concat.tree \ + ${basedir}/${species}/Roary/output/core_gene_alignment_renamed.tree \ + ${basedir}/${species}/Comparison/GFs/CG/msa_genapi/concat.tree \ + ${basedir}/${species}/Comparison/GFs/CG/msa_panaroo/concat.tree \ + -r ${basedir}/${sp}/1/Comparison/GFs/CG/msa_prova/${sp}.tree --unrooted > ${basedir}/${species}/Comparison/ete3.log + done +done diff --git a/analysis_scripts/run_fasttree.sh b/analysis_scripts/run_fasttree.sh new file mode 100755 index 0000000..0083fb5 --- /dev/null +++ b/analysis_scripts/run_fasttree.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +basedir=${PWD} +species=$1 +faa=$2 +out=$3 + +./../FastTree -gtr -nt ${faa} > ${out} + diff --git a/analysis_scripts/run_mafft.sh b/analysis_scripts/run_mafft.sh new file mode 100755 index 0000000..d80c98f --- /dev/null +++ b/analysis_scripts/run_mafft.sh @@ -0,0 +1,13 @@ +#!/bin/bash + +basedir=${PWD} +species=$1 +faa=$2 +out=$3 + +echo ${basedir} +echo $species +echo ${faa} + +mafft ${faa} > ${out} + diff --git a/process_metagenomes.ipynb b/process_metagenomes.ipynb index 912eb4e..46870cd 100644 --- a/process_metagenomes.ipynb +++ b/process_metagenomes.ipynb @@ -1412,7 +1412,7 @@ "source": [ "import subprocess\n", "faa_reference = prokkadir+'/prokka_'+ref_genome+'/*.faa'\n", - "ret=subprocess.call(['bash',basedir+\"/run_diamond.sh\",species,faa_reference],stdout=subprocess.DEVNULL)" + "ret=subprocess.call(['bash',basedir+\"/analysis_scripts/run_diamond.sh\",species,faa_reference],stdout=subprocess.DEVNULL)" ] }, { diff --git a/synthetic_trees.ipynb b/synthetic_trees.ipynb deleted file mode 100644 index 2e29bab..0000000 --- a/synthetic_trees.ipynb +++ /dev/null @@ -1,218378 +0,0 @@ -{ - "cells": [ - { - "attachments": {}, - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Building and comparing trees\n", - "The main steps for building trees are the following:\n", - "1) Retrieve core genes from a tool and save each GF to a file\n", - "2) Align core genes from each family (using mafft)\n", - "3) Concatenate alignments \n", - "4) Run maximum-likelihood tree building (FastTree)\n", - "5) Substitute genoome names such that they correspond between all tools\n", - "6) Compare phylogenies using ete3 nRF." - ] - }, - { - "cell_type": "code", - "execution_count": 48, - "metadata": {}, - "outputs": [], - "source": [ - "import subprocess\n", - "import pandas as pd\n", - "import os" - ] - }, - { - "attachments": {}, - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## PANPROVA\n", - "Ground truth trees are built starting from the core genes of the complete genomes of the synthetic benchmark, PANPROVA." - ] - }, - { - "cell_type": "code", - "execution_count": 67, - "metadata": {}, - "outputs": [], - "source": [ - "\n", - "for species in ['synth_ecoli','synth_myco','synth_paeru']:\n", - " basedir=os.getcwd()\n", - " ipanprova = basedir+'/PANPROVA_'+species+'/1/survival_families' \n", - "\n", - " CG_dir = basedir+'/'+species+'/1/Comparison/CG'\n", - " os.makedirs(CG_dir,exist_ok=True)\n", - " os.makedirs(CG_dir+'/fasta_prova',exist_ok=True)\n", - " gf_cg_prova = set()\n", - " for line in open(ipanprova,'r'):\n", - " cc = line.strip().split(' ')[1:]\n", - " \n", - " genomes = set()\n", - " cc_filt=set()\n", - " for c in cc:\n", - " genome = c.split(',')[0].lstrip('(')\n", - " if genome not in genomes:\n", - " genomes.add(genome)\n", - " cc_filt.add((c))\n", - "\n", - " size = len(genomes)\n", - " if size == 10:\n", - " gf_cg_prova.add(tuple(cc_filt))\n", - "\n", - " # read all genes\n", - " gene2seq=dict()\n", - " ipanprova_blastdb = basedir+'/PANPROVA_'+species+'/1/blastdb/'\n", - " for file in os.listdir(ipanprova_blastdb):\n", - " if file.endswith('fna'):\n", - " with open(ipanprova_blastdb+'/'+file) as f:\n", - " lines = f.readlines()\n", - " for l in lines:\n", - " if l.startswith('>'):\n", - " gene_name = l[1:].rstrip()\n", - " else: \n", - " gene2seq[gene_name]=l.rstrip()\n", - " \n", - " # write to file\n", - " i = 0 \n", - " for family in gf_cg_prova:\n", - " with open(CG_dir+'/fasta_prova/fam_'+str(i)+'.fa','w') as f:\n", - " i += 1\n", - " for gene in family: \n", - " f.write('>'+str(gene)+'\\n')\n", - " f.write(str(gene2seq[gene])+'\\n')\n", - "\n", - " # RUN MAFFT\n", - " cg_fa_prova = CG_dir+'/fasta_prova/'\n", - " msa_prova = CG_dir+'/msa_prova/'\n", - " os.makedirs(msa_prova,exist_ok=True)\n", - "\n", - " for f in os.listdir(CG_dir+'/fasta_prova/'):\n", - " if f not in os.listdir(CG_dir+'/msa_prova/'):\n", - " et=subprocess.call(['bash',basedir+\"/run_mafft.sh\",species,cg_fa_prova+f,msa_prova+f],stdout=subprocess.DEVNULL)\n", - " \n", - " # Concatenate alignments\n", - " genome2seqs=dict()\n", - " for file in os.listdir(msa_prova):\n", - " with open(msa_prova+file) as f:\n", - " lines=f.readlines()\n", - " genome=lines[0].split(',')[0].lstrip('>(')\n", - " seq=''\n", - " for l in lines[1:]:\n", - " if l.startswith('>'):\n", - "\n", - " if genome in genome2seqs:\n", - " genome2seqs[genome]=genome2seqs[genome]+seq \n", - " else:\n", - " genome2seqs[genome]=seq\n", - " seq=''\n", - " genome=l.split(',')[0].lstrip('>(')\n", - "\n", - " else:\n", - " seq+=l.strip()\n", - " \n", - "\n", - " if genome in genome2seqs:\n", - " genome2seqs[genome]=genome2seqs[genome]+seq \n", - " else:\n", - " genome2seqs[genome]=seq\n", - " \n", - " #check all went well\n", - " for g in genome2seqs:\n", - " print(len(genome2seqs[g]))\n", - "\n", - " #write to file\n", - " with open(msa_prova+'concat.msa','w') as f:\n", - " for g in genome2seqs:\n", - " f.write('>'+g+'\\n')\n", - " f.write(str(genome2seqs[g])+'\\n')\n", - " \n", - " # Build tree\n", - " ret=subprocess.call(['bash',basedir+\"/run_fasttree.sh\",species,msa_prova+'concat.msa',msa_prova+'concat.tree'],stdout=subprocess.DEVNULL)" - ] - }, - { - "attachments": {}, - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# DELOS TREE" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "basedir=os.getcwd()\n", - "\n", - "for sp in ['synth_myco','synth_ecoli','synth_paeru']:\n", - " for frag in ['0.5','0.8','1']:\n", - " species= sp+'/'+frag\n", - " delosdir = basedir+'/'+species+'/PanDelos'\n", - "\n", - " ref_to_genes_delos = dict() # #used for looking at the distribution of GF size, based on their gene in the reference genome\n", - " gf_sizes_delos = dict() #used for looking at the distribution of GF size, regardless of their association to a common gene in the reference genome\n", - "\n", - " # PanDelos\n", - " with open(delosdir+\"/output/output.clus\") as f:\n", - " lines = f.readlines()\n", - "\n", - " cg_delos=set()\n", - " for l in lines: \n", - " l = l.rstrip()\n", - " l = l.split(' ')\n", - " genome_set = set()\n", - " selected_genes = []\n", - " for gene in l:\n", - " genome = gene.split(':')[0] \n", - " if genome in genome_set:\n", - " continue\n", - " else:\n", - " genome_set.add(genome)\n", - " selected_genes.append(gene)\n", - "\n", - " if len(selected_genes)==10:\n", - " cg_delos.add(tuple(selected_genes)) \n", - "\n", - " # write to file core genes \n", - " frag_dir = delosdir+'/output/fragmented_coordinates/'\n", - " records_pan = {}\n", - " for d in os.listdir(frag_dir):\n", - " with open(frag_dir+d+'/'+\"coordinates_frag.sam\") as f:\n", - " lines = f.readlines()\n", - " for l in lines:\n", - " if l.startswith('@'):\n", - " continue\n", - " l = l.split('\\t')\n", - " name = l[0]\n", - " seq = l[9]\n", - " records_pan[name] = seq\n", - "\n", - " comparisondir = basedir+'/'+species+'/Comparison'\n", - " CG_dir = basedir+'/'+species+'/Comparison/GFs/CG'\n", - "\n", - " GF_dir = comparisondir+'/GFs'\n", - " os.makedirs(CG_dir,exist_ok=True)\n", - " os.makedirs(CG_dir+'/fasta_delos',exist_ok=True)\n", - "\n", - " i = 0 \n", - " for family in cg_delos:\n", - " with open(CG_dir+'/fasta_delos/fam_'+str(i)+'.fa','w') as f:\n", - " i += 1\n", - " for gene in family: \n", - " f.write('>'+gene+'\\n')\n", - " f.write(str(records_pan[gene])+'\\n')\n", - "\n", - "\n", - " # RUN MAFFT\n", - " import subprocess\n", - "\n", - " comparisondir = basedir+'/'+species+'/Comparison'\n", - " CG_dir = basedir+'/'+species+'/Comparison/GFs/CG'\n", - " cg_fa_delos = CG_dir+'/fasta_delos/'\n", - " msa_delos = CG_dir+'/msa_delos/'\n", - " os.makedirs(msa_delos,exist_ok=True)\n", - "\n", - " for f in os.listdir(cg_fa_delos):\n", - " if f not in os.listdir(msa_delos):\n", - " ret=subprocess.call(['bash',basedir+\"/run_mafft.sh\",species,cg_fa_delos+f,msa_delos+f],stdout=subprocess.DEVNULL)\n", - "\n", - " #CONCATENATE\n", - " genome2seqs=dict()\n", - " for file in os.listdir(msa_delos):\n", - " with open(msa_delos+file) as f:\n", - " lines=f.readlines()\n", - " genome=lines[0].split(':')[0]\n", - " seq=''\n", - " for l in lines[1:]:\n", - " if l.startswith('>'):\n", - "\n", - " if genome in genome2seqs:\n", - " genome2seqs[genome]=genome2seqs[genome]+seq \n", - " else:\n", - " genome2seqs[genome]=seq\n", - " seq=''\n", - " genome=l.split(':')[0]\n", - " else:\n", - " seq+=l.strip()\n", - " \n", - "\n", - " if genome in genome2seqs:\n", - " genome2seqs[genome]=genome2seqs[genome]+seq \n", - " else:\n", - " genome2seqs[genome]=seq\n", - "\n", - " #check all went well \n", - " for g in genome2seqs:\n", - " print(len(genome2seqs[g]))\n", - " \n", - " # read pandelos file to associate pandelos aliases to genome name\n", - " genome_names = os.listdir(delosdir+'/output/fragmented')\n", - " matchfile='predictedCDSs_filtered_only_genes.bed'\n", - " dict_list_names = []\n", - "\n", - " for g in genome_names:\n", - " files = os.listdir(delosdir+'/output/fragmented/' + g + '/artifacts')\n", - " afile = [f for f in files if f.endswith(matchfile)][0]\n", - " with open(delosdir+'/output/fragmented/' + g + '/artifacts/' +afile) as f:\n", - " delos_name = f.readline().split('\\t')[0]\n", - " \n", - " dict_row = {'genome':g, 'pandelos_name':delos_name}\n", - " dict_list_names.append(dict_row)\n", - " \n", - " names_df=pd.DataFrame(dict_list_names)\n", - " names_df\n", - "\n", - " delos2prova = dict()\n", - " for r in names_df.index:\n", - " delos2prova[names_df.loc[r,'pandelos_name']]=names_df.loc[r,'genome']\n", - "\n", - " #write to file\n", - " with open(msa_delos+'concat.msa','w') as f:\n", - " for g in genome2seqs:\n", - " f.write('>'+delos2prova[g.lstrip('>')].split('_')[1]+'\\n')\n", - " f.write(str(genome2seqs[g])+'\\n')\n", - " \n", - " # build tree\n", - " ret=subprocess.call(['bash',basedir+\"/run_fasttree.sh\",species,msa_delos+'concat.msa',msa_delos+'concat_renamed.tree'],stdout=subprocess.DEVNULL)" - ] - }, - { - "attachments": {}, - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Roary Trees" - ] - }, - { - "cell_type": "code", - "execution_count": 62, - "metadata": {}, - "outputs": [], - "source": [ - "for sp in ['synth_paeru','synth_myco','synth_ecoli']:\n", - " for frag in ['0.5','0.8','1']:\n", - " species=sp+'/'+frag\n", - " alndir = basedir+'/'+species+'/Roary/output/' # core gene alignment is already provided by Roary\n", - " #ret=subprocess.call(['bash',basedir+\"/run_fasttree.sh\",species,alndir+'core_gene_alignment.aln',alndir+'core_gene_alignment.tree'],stdout=subprocess.DEVNULL)\n", - "\n", - " with open(alndir+'core_gene_alignment.tree') as infile, open(alndir+'core_gene_alignment_renamed.tree', 'w') as outfile:\n", - " for line in infile:\n", - " line = line.replace('prokka_genome_','')\n", - " line = line.replace('_fr.fasta','')\n", - "\n", - " outfile.write(line)" - ] - }, - { - "attachments": {}, - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# GenAPI Trees" - ] - }, - { - "cell_type": "code", - "execution_count": 37, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1915\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2533\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2539\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2350\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2347\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2299\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2302\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2068\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2680\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2686\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2251\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2257\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2050\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2848\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2836\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2395\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2395\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 4063\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 4063\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1543\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1546\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2494\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2491\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3175\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3175\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3190\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3190\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2755\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2206\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2161\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1972\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1912\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1903\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1682\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1667\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2137\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2137\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3124\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3112\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2674\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2674\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2155\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2233\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2233\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1831\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2752\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2539\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1963\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1771\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1783\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3745\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3742\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3874\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3874\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2647\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2650\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2257\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2254\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "62440\n", - "62440\n", - "62440\n", - "62440\n", - "62440\n", - "62440\n", - "62440\n", - "62440\n", - "62440\n", - "62440\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2332\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2317\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2299\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2299\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2449\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2449\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3874\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3874\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2989\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2995\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2455\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2464\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3103\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3106\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2842\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2845\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1528\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3223\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3223\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3850\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3832\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2626\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2626\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2137\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2137\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2137\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2134\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 4063\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 4063\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1543\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2050\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2533\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2539\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1789\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1789\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2647\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2650\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1750\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1747\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2395\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2395\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2755\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1543\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1546\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2848\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2836\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2068\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2791\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2782\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1963\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2350\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2347\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3055\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3055\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2176\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2173\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2188\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2188\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1582\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1585\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2674\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2674\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1444\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1444\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1972\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1990\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1978\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1990\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2494\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2491\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3280\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3277\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1831\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1945\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2389\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2389\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1450\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2299\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2302\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2305\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2308\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3175\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3175\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1612\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2011\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2017\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1682\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1667\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1879\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2155\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2680\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2686\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2206\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1831\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1834\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2752\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1915\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2704\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2692\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3745\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3742\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1672\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1672\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2446\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2434\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2251\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2257\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2302\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2302\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2116\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2095\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1570\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1570\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1765\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1768\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2185\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2233\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2233\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2794\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2794\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3190\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3190\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3124\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3112\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1693\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1693\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2257\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2254\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1816\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1819\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1771\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1783\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2785\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2785\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1381\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1375\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2755\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2743\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1912\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1903\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "119930\n", - "119930\n", - "119930\n", - "119930\n", - "119930\n", - "119930\n", - "119930\n", - "119930\n", - "119930\n", - "119930\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3745\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3742\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2899\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2887\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2365\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2365\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1570\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1570\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2215\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2215\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3175\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3175\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1912\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1903\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2794\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2794\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2830\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2827\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1963\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2848\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2836\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2155\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2137\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1648\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1648\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1873\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1870\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2068\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1693\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1690\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1990\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1978\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1492\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1489\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1789\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1789\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2929\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2929\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2704\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2692\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2299\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2299\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1612\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2647\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2647\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1501\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1501\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1891\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2389\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2383\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1765\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1768\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3223\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3223\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2446\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2434\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3142\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3148\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2539\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2536\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2380\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2383\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2674\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2674\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1816\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1819\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2257\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2254\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3280\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3277\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3124\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3112\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1972\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1672\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1672\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1831\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1834\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2017\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2017\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 4918\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 4918\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2176\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2173\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1705\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1699\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2827\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2827\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3874\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3874\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2827\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2827\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2116\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2095\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2329\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2329\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1915\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1918\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1732\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1738\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3739\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3739\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2485\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2485\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1381\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1375\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2500\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2497\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2647\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2650\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2755\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2743\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1682\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1667\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2185\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2233\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2233\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3256\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3289\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2842\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2854\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2167\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2170\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2647\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2650\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 4063\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 4063\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2971\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2965\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2989\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2995\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1879\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2251\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2257\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2137\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2134\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2455\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2464\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1693\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1693\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1945\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1597\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1603\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2017\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2017\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1990\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2284\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2284\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1771\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1783\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2083\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2083\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2395\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2395\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3190\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3190\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2785\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2785\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2011\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2017\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2299\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2302\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1528\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1414\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1411\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3280\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3298\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1672\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1672\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1690\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1690\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2362\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2353\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1444\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1444\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2137\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2137\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2866\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2833\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2533\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2539\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2164\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2161\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2479\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2479\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2764\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2713\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1537\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1537\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2680\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2686\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1543\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3850\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3832\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1765\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1765\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2332\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2317\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3055\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3055\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1903\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1630\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1624\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1873\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1873\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2014\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2014\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1450\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1930\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1930\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2755\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2050\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2041\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2449\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2449\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2206\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2389\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2389\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2494\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2491\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1879\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1903\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2953\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2956\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2305\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2308\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2299\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2302\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1696\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1684\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2275\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2275\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1645\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1633\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1582\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1585\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1570\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1570\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2350\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2347\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2302\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2302\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1750\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1747\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3484\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3478\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1603\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1594\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2260\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2272\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2278\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2281\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1414\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1411\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1831\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2920\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2920\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3103\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3106\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2188\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2188\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1879\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1879\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2155\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2050\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1543\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1546\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2572\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2572\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2842\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2845\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2791\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2782\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2245\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2248\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2752\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2473\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2464\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "211582\n", - "211582\n", - "211582\n", - "211582\n", - "211582\n", - "211582\n", - "211582\n", - "211582\n", - "211582\n", - "211582\n" - ] - } - ], - "source": [ - "import pandas as pd\n", - "import os\n", - "import numpy as np\n", - "import re\n", - "basedir=os.getcwd()\n", - "\n", - "for sp in ['synth_paeru']:\n", - " for frag in ['0.5','0.8','1']:\n", - " species=sp+'/'+frag\n", - "\n", - " prokkadir= basedir+'/'+species+'/Prokka' \n", - " gene2seq = dict()\n", - "\n", - " for file in os.listdir(prokkadir):\n", - " all_files = os.listdir(prokkadir+'/'+file)\n", - " ffn_file = [f for f in all_files if f.endswith('ffn')][0]\n", - " with open(prokkadir+'/'+file+'/'+ffn_file) as f:\n", - " lines=f.readlines()\n", - " gene=lines[0].split(' ')[0]\n", - " seq=''\n", - " for l in lines[1:]:\n", - " if l.startswith('>'):\n", - " gene2seq[gene]=seq\n", - " gene=l.split(' ')[0]\n", - " seq=''\n", - " else:\n", - " seq+=l.strip()\n", - " gene2seq[gene]=seq\n", - "\n", - "\n", - " itool = basedir+'/'+species+'/GenAPI/clustered_genes_genapi.ffn.clstr'\n", - " gf2genes=dict()\n", - " with open(itool,'r') as f:\n", - " lines = f.readlines()\n", - " GF_name=lines[0].lstrip('>').split(' ')[1].rstrip()\n", - " GF_list=[]\n", - " genomes=set()\n", - " CG=False\n", - "\n", - " for l in lines[1:]:\n", - " if l.startswith('>'):\n", - " if len(GF_list) == 10 and CG == True:\n", - " gf2genes[GF_name]=GF_list\n", - " GF_name=l.lstrip('>').split(' ')[1].rstrip()\n", - " CG = True\n", - " genomes=set()\n", - " GF_list=[]\n", - " else:\n", - " gene= l.split('>')[1].split(':')[0]\n", - " genome=gene.split('_')[0]\n", - " if genome in genomes:\n", - " CG=False\n", - " genomes.add(genome)\n", - " GF_list.append(gene)\n", - "\n", - " CG_dir = basedir+'/'+species+'/Comparison/GFs/CG'\n", - "\n", - " os.makedirs(CG_dir+'/fasta_genapi',exist_ok=True)\n", - " for gf in gf2genes: \n", - " genes=gf2genes[gf]\n", - "\n", - " with open(CG_dir+'/fasta_genapi/'+gf+'.fa','w') as f:\n", - " for g in genes:\n", - " f.write('>'+g+'\\n')\n", - " f.write(str(gene2seq['>'+g])+'\\n') \n", - " # RUN MAFFT\n", - " import subprocess\n", - " cg_fa_genapi = CG_dir+'/fasta_genapi/'\n", - " msa_genapi = CG_dir+'/msa_genapi/'\n", - " os.makedirs(msa_genapi,exist_ok=True)\n", - "\n", - " for f in os.listdir(cg_fa_genapi):\n", - " ret=subprocess.call(['bash',basedir+\"/run_mafft.sh\",species,cg_fa_genapi+f,msa_genapi+f],stdout=subprocess.DEVNULL)\n", - " # Concatenate alignments\n", - " genome2seqs=dict()\n", - " for file in os.listdir(msa_genapi):\n", - " with open(msa_genapi+file) as f:\n", - " lines=f.readlines()\n", - " genome=lines[0].split('_')[0]\n", - " seq=''\n", - " for l in lines[1:]:\n", - " if l.startswith('>'):\n", - "\n", - " if genome in genome2seqs:\n", - " genome2seqs[genome]=genome2seqs[genome]+seq \n", - " else:\n", - " genome2seqs[genome]=seq\n", - " seq=''\n", - " genome=l.split('_')[0]\n", - " else:\n", - " seq+=l.strip()\n", - " \n", - "\n", - " if genome in genome2seqs:\n", - " genome2seqs[genome]=genome2seqs[genome]+seq \n", - " else:\n", - " genome2seqs[genome]=seq\n", - " #check all went well \n", - " for g in genome2seqs:\n", - " print(len(genome2seqs[g]))\n", - " #write to file\n", - " with open(msa_genapi+'concat.msa','w') as f:\n", - " for g in genome2seqs:\n", - " f.write(g+'\\n')\n", - " f.write(str(genome2seqs[g])+'\\n')\n", - "\n", - " # Build tree\n", - " ret=subprocess.call(['bash',basedir+\"/run_fasttree.sh\",species,msa_genapi+'concat.msa',msa_genapi+'concat.tree'],stdout=subprocess.DEVNULL)\n", - "\n", - " # Change names of genomes to correposnd to PANPROVA genomes\n", - " roary2genome = dict()\n", - " genome_names = os.listdir(delosdir+'/output/fragmented')\n", - " matchfile='predictedCDSs_filtered_only_genes.bed'\n", - " dict_list_names = [] \n", - " prokka_dirs=os.listdir(prokkadir)\n", - " for genome_full in prokka_dirs:\n", - " genome=genome_full.split('_')[2]\n", - " files=os.listdir(prokkadir+'/'+genome_full)\n", - " index_tsv = [i for i,name in enumerate(files) if re.search(\"tsv\", name)][0]\n", - "\n", - " with open(prokkadir+'/'+genome_full+'/'+files[index_tsv]) as f:\n", - " code=f.readlines()[1].split('\\t')[0].split('_')[0]\n", - " \n", - " roary2genome[code]=genome\n", - "\n", - " # Rename tree\n", - " with open(msa_genapi+'concat.tree') as infile, open(msa_genapi+'concat_renamed.tree', 'w') as outfile:\n", - " for line in infile:\n", - " for src, target in roary2genome.items():\n", - " line = line.replace(src, target)\n", - " outfile.write(line)" - ] - }, - { - "attachments": {}, - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Panaroo trees" - ] - }, - { - "cell_type": "code", - "execution_count": 45, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "synth_myco/0.5/\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "249\n", - "249\n", - "249\n", - "249\n", - "249\n", - "249\n", - "249\n", - "249\n", - "249\n", - "249\n", - "synth_myco/0.8/\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1912\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1471\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1474\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1363\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1363\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1423\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1423\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1525\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1954\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1954\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "8121\n", - "8121\n", - "8121\n", - "8121\n", - "8121\n", - "8121\n", - "8121\n", - "8121\n", - "8121\n", - "8121\n", - "synth_myco/1/\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1852\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1912\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1576\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1582\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1471\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1465\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2620\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1915\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1915\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1711\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1744\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1744\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1399\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1399\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1342\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1339\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1384\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1387\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1738\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1735\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1618\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1363\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1363\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2827\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2827\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1699\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1696\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1423\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1423\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2113\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2113\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1645\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1648\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1510\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1510\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1321\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1321\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1669\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1675\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1396\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2941\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2929\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1768\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1768\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1660\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1663\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2581\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2578\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1486\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1486\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1477\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1477\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1615\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1615\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1387\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1423\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1525\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1954\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1954\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " 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distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1471\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1474\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "34245\n", - "34245\n", - "34245\n", - "34245\n", - "34245\n", - "34245\n", - "34245\n", - "34245\n", - "34245\n", - "34245\n", - "synth_ecoli/0.5/\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1321\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1321\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2710\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2707\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1438\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1435\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2101\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2110\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1807\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1807\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2554\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2554\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3901\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3901\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1642\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1642\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2068\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1408\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1408\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 4111\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 4117\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1990\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1444\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1555\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1555\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1642\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1756\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1756\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2416\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2416\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2086\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2089\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1705\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1705\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1663\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1663\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2224\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "19046\n", - "19046\n", - "19046\n", - "19046\n", - "19046\n", - "19046\n", - "19046\n", - "19046\n", - "19046\n", - "19046\n", - "synth_ecoli/0.8/\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2224\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2113\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1948\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2404\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2404\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3922\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3922\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2719\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2719\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1921\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1921\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1810\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1813\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1567\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1978\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2254\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2251\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1909\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1909\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1819\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2107\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2107\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1930\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1933\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1870\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2257\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2260\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1747\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1750\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2050\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2050\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1729\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1729\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2248\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2248\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1603\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1603\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1744\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1744\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1762\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1762\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1789\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1789\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2047\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2047\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2149\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2158\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3877\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3877\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2299\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2269\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1462\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1462\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1846\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1852\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1720\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1720\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2503\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2485\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1672\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1561\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1564\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1564\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1564\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2146\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2131\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2143\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2170\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2089\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2089\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2209\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2209\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3562\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3562\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3070\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3055\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1705\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1708\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1465\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1642\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1762\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2242\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2242\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1699\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1858\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1840\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2014\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2014\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3184\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3184\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2068\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1561\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1561\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1954\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1948\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2086\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2089\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2710\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2707\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3901\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3901\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3304\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3286\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1816\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1813\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2917\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2899\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1774\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1774\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1495\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1498\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2107\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2107\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2380\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2380\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1726\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1735\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 4063\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 4066\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1375\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1378\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2116\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2116\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1687\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1687\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2785\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2785\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1621\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1711\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1711\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1456\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1456\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1963\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1963\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3367\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3367\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3376\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3403\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1474\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1471\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1612\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1612\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1705\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1708\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2206\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2206\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1966\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2131\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2131\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2758\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2758\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2863\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2845\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2467\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2467\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2422\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2422\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2266\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2266\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1942\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1942\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2134\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2155\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1666\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1663\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1624\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1579\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1579\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2686\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2662\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1402\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1402\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1999\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1999\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1957\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1780\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1777\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1693\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1696\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2344\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2344\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2065\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2056\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1705\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1705\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1408\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1408\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1525\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1915\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2803\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2803\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1429\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1429\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2860\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2860\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3199\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3202\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1468\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1582\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1579\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1486\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1486\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1804\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1807\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2968\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2968\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2497\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2497\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1705\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1699\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1912\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1912\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1417\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2212\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2212\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1585\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1585\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2941\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2941\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2428\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2428\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1603\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1879\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1879\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2218\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1501\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1369\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1363\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1507\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1513\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1891\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1903\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1438\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1438\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1699\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1690\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2470\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2452\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1978\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1384\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1381\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1510\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1507\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1477\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1480\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2464\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2464\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2068\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3385\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3385\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2329\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2317\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2230\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2230\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2092\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2092\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2317\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2317\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1846\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1471\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1471\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3472\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3472\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1558\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1558\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2482\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2482\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1990\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1933\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2584\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2584\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1432\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1432\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1648\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1648\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1411\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1411\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2644\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2644\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2554\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2554\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2020\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2011\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3349\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3349\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1756\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1756\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2576\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2581\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2614\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2416\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2416\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1474\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1474\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1729\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1732\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1819\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2326\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2338\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3325\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3325\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2119\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2641\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2641\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2287\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2278\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1606\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1606\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1642\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1561\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1561\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2089\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2083\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2257\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2257\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2473\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2473\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2500\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2512\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1552\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1555\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1591\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1597\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1696\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1696\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1579\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1582\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1690\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1690\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1441\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1441\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3142\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3142\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1537\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1537\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1648\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1648\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2608\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2608\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2245\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2251\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2041\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1705\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1873\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2209\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2227\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1651\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1651\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1933\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1933\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1333\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1333\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3784\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3751\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1450\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1450\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2287\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2287\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2578\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2578\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3310\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3310\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2176\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2332\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2305\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "168773\n", - "168773\n", - "168773\n", - "168773\n", - "168773\n", - "168773\n", - "168773\n", - "168773\n", - "168773\n", - "168773\n", - "synth_ecoli/1/\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2632\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2656\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2239\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2242\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1846\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1846\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2023\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2029\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2344\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2353\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2860\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2860\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2113\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1948\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1345\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1345\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1456\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1456\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2443\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2443\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2101\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1423\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1423\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1642\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1642\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2440\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2440\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2182\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2182\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1960\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2167\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2158\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3010\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3010\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2215\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1567\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1570\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1576\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1570\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1507\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1507\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2371\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2371\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1582\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1582\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1921\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1921\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1597\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1597\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2233\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2236\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2665\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2665\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2242\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2242\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1816\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1816\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1750\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1774\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1774\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1474\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1471\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2953\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3019\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2686\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2686\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2893\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2893\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1618\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2488\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2479\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2371\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2371\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2302\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2299\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2254\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2251\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2677\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2677\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2368\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2368\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2335\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2335\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1819\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1744\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1558\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1558\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2383\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2383\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2089\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2095\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2209\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2209\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1468\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1798\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1807\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3355\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3358\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1564\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1564\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2875\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2857\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2485\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2485\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1873\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2380\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2380\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2095\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2095\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1756\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1756\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2854\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2854\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1510\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1507\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1585\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1585\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2212\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2218\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1822\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1831\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2401\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2401\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2380\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2380\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1579\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1582\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2248\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2242\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1930\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1933\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2047\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2047\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2422\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2422\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2035\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2035\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3844\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3844\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1870\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1453\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2266\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2275\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2230\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2212\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1720\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1720\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1963\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1963\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2554\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2554\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2068\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2119\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2122\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1555\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1555\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2050\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2050\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1756\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1756\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1621\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1621\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2710\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2710\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1999\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2002\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2443\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2443\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2047\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2047\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1603\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1603\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2299\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2269\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2020\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2011\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1744\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1744\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2257\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2257\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2299\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2272\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1762\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1762\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1735\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1747\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2476\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2476\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1534\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1711\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1711\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1903\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1903\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2005\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2617\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2617\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1660\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1858\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1789\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1789\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2188\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2188\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2491\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2476\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2236\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2236\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1936\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1930\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3250\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3250\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2491\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2491\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3784\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3751\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1957\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2248\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2248\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1372\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1372\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2191\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2191\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1831\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1834\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1840\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1831\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2200\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2200\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2551\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2551\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1879\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1879\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2287\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2035\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2035\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2212\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1846\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1852\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1720\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1720\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2503\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2503\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2170\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2167\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2503\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2485\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1672\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1561\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1564\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1591\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1591\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1903\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1387\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1387\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2146\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2131\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2158\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2158\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2143\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2170\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1612\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1612\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1816\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1813\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2209\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2209\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3562\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3562\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2134\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2131\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1933\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1933\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3070\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3055\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1909\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1909\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1534\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1534\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1756\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2875\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2875\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1747\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1747\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1753\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1753\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1597\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1597\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1678\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1675\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3505\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3505\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1375\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1381\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1858\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1840\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2443\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2428\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1936\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1468\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1453\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1456\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3013\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3013\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2360\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2360\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2014\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2014\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1933\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2005\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2008\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2011\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2011\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1561\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1561\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1579\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1582\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2149\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2161\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1645\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1648\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1645\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2149\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2134\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2632\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2632\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2128\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2122\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3199\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3169\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1591\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1588\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1954\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1948\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2404\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2404\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2143\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2149\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1600\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1603\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1501\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1507\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3142\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3139\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2161\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2161\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1912\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1912\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1561\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1570\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1564\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1576\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1561\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1561\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1846\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3337\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3352\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3901\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3901\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2320\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2320\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1999\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1999\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1582\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1579\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2026\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2026\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1603\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2113\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3193\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3193\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1321\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3370\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3385\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2707\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2701\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2437\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2437\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1615\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1615\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1870\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1870\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2008\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2020\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2374\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2380\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1750\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1750\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2377\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2377\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1936\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1936\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2545\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2545\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1495\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1498\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1660\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1645\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1843\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1843\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2476\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2476\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2401\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2398\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1699\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2662\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2662\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 4063\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 4066\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2815\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2149\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2158\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1807\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1804\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3493\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3481\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1594\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1594\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2116\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2116\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1690\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1690\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1426\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1426\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1633\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1438\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1438\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1615\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1615\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1804\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1384\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1381\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1621\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1963\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1510\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1510\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1711\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1711\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2911\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2908\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2353\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2356\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2335\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2365\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1546\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1546\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2761\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2761\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2509\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2503\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2002\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2002\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2422\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2422\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2551\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2551\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1327\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1330\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2707\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2707\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1327\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1330\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1732\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2356\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2365\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1783\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2050\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2068\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1798\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1798\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1606\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1606\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2506\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2506\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1918\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1918\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1666\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1666\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1375\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1378\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1336\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1336\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1879\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3517\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3529\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1486\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1486\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1900\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1519\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3349\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3349\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1435\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1435\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1471\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1462\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2569\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2578\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2392\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2386\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1891\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2947\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2947\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1669\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1666\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2467\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2467\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3376\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3403\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2437\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2437\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1852\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1852\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2284\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2284\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1753\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1753\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2266\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2266\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1693\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1696\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1909\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1732\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1732\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3070\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3061\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2134\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2155\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1729\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1726\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1666\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1663\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3127\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3127\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2866\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2866\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2686\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2662\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1858\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2668\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2689\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1663\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1663\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1648\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1648\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2068\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1990\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1990\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1642\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2236\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2236\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1480\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1480\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2734\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2731\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1780\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1777\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1588\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1591\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1591\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1543\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1621\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1621\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3091\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3091\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1465\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1510\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1510\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1963\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1963\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1813\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1807\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2464\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2446\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1846\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2458\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2443\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1756\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1756\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1504\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1504\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1642\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1642\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1705\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1708\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1690\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1690\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2344\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2344\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2065\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2056\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1831\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2545\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2545\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2647\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2617\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1615\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1615\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2200\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2200\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3403\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3403\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2278\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2269\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2167\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1642\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1699\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1690\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2158\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2161\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1762\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1519\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1729\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1729\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2329\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2317\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2086\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2092\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2701\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2722\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3646\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3652\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1873\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1876\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1687\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1786\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1786\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2266\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2266\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2365\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2362\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1873\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1879\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2251\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2251\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1405\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1408\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2107\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2107\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1873\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2230\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2230\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2143\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2143\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2863\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2845\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2035\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2047\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1876\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1876\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1915\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2287\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2263\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1603\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1597\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1726\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1888\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1954\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2803\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2803\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1933\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1942\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1735\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1738\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1300\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1300\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1960\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1960\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2665\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2665\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2209\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2227\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3199\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3202\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1540\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1540\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2302\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2308\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2248\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2248\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2545\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2551\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1921\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1804\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1804\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2122\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2140\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1753\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1753\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2818\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2830\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1804\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1804\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2497\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2497\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1351\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1351\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2479\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2479\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3514\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3514\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1669\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1669\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1567\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1690\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1690\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1468\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1468\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1558\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1558\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1786\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1786\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1936\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1936\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1864\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3769\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3793\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1645\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2320\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2320\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2074\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2074\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2014\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2023\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1813\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1813\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1576\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1576\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1789\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1471\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1471\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2941\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2941\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2386\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2386\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2371\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2383\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2869\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2869\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2083\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2218\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1387\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1387\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2473\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2473\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3091\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3091\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1672\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1666\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3787\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3787\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1834\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1834\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1862\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2923\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2938\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1633\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1633\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1831\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2377\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2386\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2434\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2455\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2734\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2728\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1948\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1954\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1573\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1573\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2005\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1999\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1921\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1585\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1585\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1507\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1513\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1465\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1465\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1375\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1375\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1729\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2032\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2005\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1891\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1903\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2209\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2209\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1753\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1756\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1501\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1720\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1720\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1477\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1477\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1786\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1786\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2089\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2089\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2332\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2332\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1624\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2341\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2341\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1384\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1384\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1525\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2353\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2374\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2587\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2587\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1579\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1579\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2470\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2452\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1978\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 1 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 1 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1699\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1708\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1387\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1387\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2086\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2089\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1474\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1471\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1483\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1483\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2689\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2689\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1687\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1687\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1621\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1621\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1477\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1480\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2464\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2464\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2038\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2068\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3385\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3385\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2917\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2899\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2530\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2530\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1705\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1699\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1648\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1648\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2230\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2230\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2092\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2092\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2317\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2317\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2158\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2158\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2209\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2209\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2047\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2065\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1933\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1933\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3472\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3472\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1804\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1807\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2596\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2593\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2737\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2737\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1810\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1804\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1735\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1735\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2482\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2482\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1990\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1765\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1660\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1960\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1960\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2638\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2638\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2617\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2617\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1873\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1876\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3562\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3571\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2164\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2170\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2584\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2584\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1432\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1432\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2071\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2065\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2644\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2644\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2050\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2068\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1834\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1834\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2002\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2002\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2320\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2320\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1435\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2608\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2449\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2425\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1819\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3067\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3049\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2029\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2026\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1735\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1720\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2266\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1669\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1669\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1864\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1891\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1756\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1756\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1483\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1480\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2576\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2581\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3379\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3379\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2170\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2167\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1720\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1720\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2758\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2758\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1864\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2180\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2185\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3049\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2416\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2416\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1921\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2257\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2260\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2143\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2143\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2728\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2728\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3118\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3115\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1966\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1576\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1576\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2371\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2362\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1606\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1606\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2494\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2509\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1651\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1651\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1474\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1474\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3004\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3004\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1597\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1597\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1438\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1438\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1852\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1705\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1702\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1819\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1774\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1315\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1315\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1699\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1705\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1693\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1693\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2326\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2338\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3325\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3325\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1510\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1510\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2287\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2287\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1702\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1693\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1705\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1435\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1435\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1573\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1573\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1690\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1690\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2488\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2473\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1537\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1537\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2746\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2746\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1651\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2797\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2797\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1408\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1408\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2587\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2599\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2641\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2641\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1345\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2287\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2278\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1921\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1915\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1411\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1411\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1966\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1963\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2428\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2428\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1738\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2806\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2794\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2644\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2623\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2374\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2374\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2092\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1444\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1444\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2407\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2407\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1765\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1771\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2089\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2083\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2008\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2008\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2197\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2182\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3934\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3934\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1642\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1978\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1978\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1417\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1603\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1603\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1873\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1873\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2257\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2257\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1753\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1756\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2377\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2377\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2500\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2512\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3463\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3463\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2140\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2140\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2206\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2206\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1552\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1555\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1771\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1768\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1591\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1597\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1570\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1567\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1675\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1675\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1411\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1408\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1822\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1822\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2206\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2206\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1696\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1696\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1747\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1750\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1594\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1591\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2056\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1873\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2353\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2341\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1579\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1579\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1561\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1561\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2656\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2650\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1642\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2197\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2197\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2002\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2011\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1870\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1870\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2188\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2188\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1537\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1537\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2587\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2578\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2608\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2608\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2245\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2251\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2572\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2572\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2137\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2146\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1957\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1960\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2224\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2224\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1999\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1999\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1915\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1915\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1720\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3070\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3109\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2041\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2431\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2431\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2719\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2719\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1705\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1864\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3877\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3877\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1873\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1543\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1540\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2998\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3001\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1555\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1555\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2164\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2968\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2968\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2941\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2941\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1873\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1573\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1582\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1687\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1687\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1333\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1333\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2107\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2107\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1525\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1525\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1585\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1588\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2296\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2281\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2320\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2320\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1327\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1327\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1441\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1441\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1804\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1807\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1786\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1798\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1225\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1225\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1399\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1396\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2269\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2272\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2578\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2578\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3310\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3310\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2176\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2224\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1441\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1441\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "557464\n", - "557464\n", - "557464\n", - "557464\n", - "557464\n", - "557464\n", - "557464\n", - "557464\n", - "557464\n", - "557464\n", - "synth_paeru/0.5/\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1705\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1705\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1612\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1612\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1948\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1945\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1504\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1495\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2086\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2086\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1705\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1435\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1435\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2332\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2305\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2032\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2035\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2392\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2392\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1888\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1888\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3802\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3802\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1471\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1471\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2113\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2113\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2359\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2359\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1543\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1546\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1597\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1597\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1546\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1540\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2038\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2032\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3034\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3007\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2836\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2836\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2461\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2467\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2506\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2509\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2851\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2836\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2233\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2233\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2023\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2026\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2551\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2560\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2218\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1957\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1957\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1594\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1594\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2452\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2440\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1543\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1945\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1933\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2032\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2032\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1501\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1498\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3346\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3337\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1918\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1918\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2821\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2821\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1972\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2269\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2224\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2236\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3724\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3724\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2050\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2158\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2161\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1711\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1711\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3298\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3298\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3121\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3121\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1963\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1978\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1831\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2704\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2704\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1684\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1669\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1768\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1765\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1834\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1834\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1366\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1357\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2788\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2770\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3190\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3190\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2347\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2329\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2188\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1492\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1492\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2161\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2860\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2860\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2050\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2584\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2584\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1660\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1840\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1840\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2137\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2137\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2083\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2083\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1423\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1423\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1666\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1732\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1732\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1495\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1495\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1915\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2497\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2497\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1813\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1813\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2359\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2335\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2140\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2134\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3091\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3091\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1900\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1900\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1846\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1846\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1789\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1682\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1667\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2017\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2020\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1483\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1483\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1750\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1744\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1963\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1960\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2653\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2638\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1495\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1489\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1771\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1783\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1978\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3790\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3790\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2533\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2533\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2614\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2599\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2539\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2176\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2167\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2884\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2887\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2680\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2686\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2197\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2197\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2770\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2779\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2119\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2128\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2431\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2431\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1675\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1675\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1900\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1999\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2953\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2953\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2332\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2335\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2629\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2614\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1435\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1435\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2548\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2563\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2653\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2653\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1663\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1651\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2047\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2911\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2908\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3073\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3073\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2863\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2863\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3877\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3865\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1786\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1786\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2206\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2155\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1678\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1672\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1498\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1498\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2395\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2395\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2014\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2014\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1726\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1726\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1957\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1945\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2107\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2107\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2023\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2023\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2674\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2674\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1201\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1912\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1903\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2500\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2500\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1261\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1261\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "125410\n", - "125410\n", - "125410\n", - "125410\n", - "125410\n", - "125410\n", - "125410\n", - "125410\n", - "125410\n", - "125410\n", - "synth_paeru/0.8/\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1900\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2647\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2650\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1363\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1363\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2317\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2317\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1807\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3586\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3589\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1750\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1747\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2548\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2563\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3436\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3442\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2653\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2653\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1519\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1519\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1891\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3196\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3196\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2167\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2167\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1423\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1423\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2305\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2308\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1411\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1411\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2692\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2680\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2836\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2836\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3034\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3007\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1720\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1684\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1669\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1636\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1636\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2863\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2863\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1579\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1579\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2086\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 4636\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 4636\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2884\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2812\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1687\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1693\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3481\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3481\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1423\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1423\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2851\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2836\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2521\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2500\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2023\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2026\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2551\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2560\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2002\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2002\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2218\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2017\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2017\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2323\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2320\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2023\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2023\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2503\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2506\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1495\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1495\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1840\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1594\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1594\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2689\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2689\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1564\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1564\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2452\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2440\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1786\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1786\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1543\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2071\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1945\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1933\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2032\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2032\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3103\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3106\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1930\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2218\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2218\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1918\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1918\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1501\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1498\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2821\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2821\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2101\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2092\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1567\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1561\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1972\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1813\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1813\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2269\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2176\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2167\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2038\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2032\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2224\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2236\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1675\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1675\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1696\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1696\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1789\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1789\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2602\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2602\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3784\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3826\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1801\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1819\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2572\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2572\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3121\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3121\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3724\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3724\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2794\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2794\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2005\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2005\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2083\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2083\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1660\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1933\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2422\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2428\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2011\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2017\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2704\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2704\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1651\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2011\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2011\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1963\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1963\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1960\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2680\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2686\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1678\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1672\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1957\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1945\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1831\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1450\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2770\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2779\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2281\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2275\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2788\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2770\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1822\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1822\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2293\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2320\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2206\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1729\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1729\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2833\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2833\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2188\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3460\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3460\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1534\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1483\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1483\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2293\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2299\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2299\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1585\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1585\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1900\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1900\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1682\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1667\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2533\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2533\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1504\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1504\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3511\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3511\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2293\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2299\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2356\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2377\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2242\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2242\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2755\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2743\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1765\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1768\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1453\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1453\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1390\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1390\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3346\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3337\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2050\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1891\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3244\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3217\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2584\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2584\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1765\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1696\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1696\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1693\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1693\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2137\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2137\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3004\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3004\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1624\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1624\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1666\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1921\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1921\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2347\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2329\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1744\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2863\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2863\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3091\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3091\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1999\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2902\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2908\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2899\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2899\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1732\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1732\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2557\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2551\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1495\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1495\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2473\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2464\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2449\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2449\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1864\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1672\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1672\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1846\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1846\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2212\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2359\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2359\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3046\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3046\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3655\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3655\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1915\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2965\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2965\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2497\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2497\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1594\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1600\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2164\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2149\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2929\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2932\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1525\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2140\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2134\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2101\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2092\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3139\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3139\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1543\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2914\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2914\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2518\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2539\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3091\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3091\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2566\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2554\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1480\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1480\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2002\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2449\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2452\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2467\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2482\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3109\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3109\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2170\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2164\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1702\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1696\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1642\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2176\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2173\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2911\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2908\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1900\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1888\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 4216\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 4225\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1444\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1444\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1990\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1546\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1540\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2476\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2476\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3190\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3190\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2110\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2110\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2017\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2020\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1771\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1783\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3073\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3073\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2008\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2020\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1840\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1840\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1768\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1768\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1612\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1516\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1516\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2671\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2704\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1789\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2473\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2479\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1573\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1567\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1261\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1261\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2524\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2524\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2653\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2638\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2764\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2731\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2428\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2428\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1810\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1816\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1201\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2083\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2089\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2158\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2158\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2491\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2491\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2155\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1840\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1381\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1375\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1525\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3874\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3874\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2368\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2368\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1675\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1675\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2086\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1498\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1498\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1978\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1615\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1615\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1750\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1756\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1420\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1417\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3790\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3790\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2056\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2068\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3067\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3067\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1489\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1489\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2449\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2449\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1750\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1744\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1513\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1513\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2113\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2113\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1786\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1786\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2272\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2278\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1726\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1726\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3043\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3028\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1876\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1873\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2116\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2095\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2884\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2887\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2197\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2197\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2224\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2041\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2041\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2368\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2362\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2050\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2035\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2035\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2119\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2128\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1591\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1591\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2158\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2161\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3280\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3277\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1582\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1585\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2233\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2233\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3298\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3298\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2953\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2953\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2332\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2335\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2629\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2614\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1753\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1753\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2386\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2386\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1435\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1435\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1888\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2098\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2098\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1663\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1651\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2149\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1492\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1492\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1480\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1486\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2608\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2092\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2089\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1831\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1834\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2161\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2173\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1945\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2074\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2071\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3439\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3439\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1957\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1957\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1813\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1813\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2260\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2260\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1768\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1765\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2446\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2434\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1750\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1750\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2989\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2995\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1762\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1762\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2626\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2626\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1528\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1963\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1978\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2317\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2320\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2281\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2257\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1834\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1834\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2416\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2416\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2527\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3445\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3445\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2860\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2860\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1597\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1597\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2437\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1999\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1999\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2701\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2701\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1999\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2395\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2395\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2614\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2599\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1864\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2566\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2578\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2014\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2014\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3850\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3832\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1726\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1726\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2107\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2107\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2848\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2866\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2533\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2551\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1543\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1546\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1495\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1489\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1990\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1978\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2674\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2674\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2155\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2155\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1780\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1780\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2359\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2335\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1912\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1903\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2500\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2500\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1555\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1555\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2779\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2776\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1366\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1357\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1576\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1579\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1399\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1399\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1816\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1819\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "319988\n", - "319988\n", - "319988\n", - "319988\n", - "319988\n", - "319988\n", - "319988\n", - "319988\n", - "319988\n", - "319988\n", - "synth_paeru/1/\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2962\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2962\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1630\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2827\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2836\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2071\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1900\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1900\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2317\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2317\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2083\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2083\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1807\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2599\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2599\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2860\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2860\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3013\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3013\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2413\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2413\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1555\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1555\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2542\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2542\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2653\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2653\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1738\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2284\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2284\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1852\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1852\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2011\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2884\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2812\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1831\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3196\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3196\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2014\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2014\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1876\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1873\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2056\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2056\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2158\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2158\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1702\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1702\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2293\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3784\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3826\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2167\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2167\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1813\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1813\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1810\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1810\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1525\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1690\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1690\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2305\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2308\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1621\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2659\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2659\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1411\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1411\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2677\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2677\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1687\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1693\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2959\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2947\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1900\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1888\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2299\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2302\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3034\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3007\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1771\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1783\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1558\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1558\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2173\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2164\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1528\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1801\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1819\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2422\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2428\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2206\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2206\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1573\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1573\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2287\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2293\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2320\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2863\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2875\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1999\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3586\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3589\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2242\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2242\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2236\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2233\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1705\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1699\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2044\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2050\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2110\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2110\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2086\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1501\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1498\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1471\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1474\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2164\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2161\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3139\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3139\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1594\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1594\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3346\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3337\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 4663\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 4675\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2629\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2629\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1678\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1675\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2251\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2257\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2311\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2311\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1918\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1918\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1702\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1699\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1682\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1667\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2902\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2908\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1870\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1870\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1732\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1738\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1918\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1918\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2728\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2731\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1597\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1603\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2038\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2038\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1690\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1684\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2365\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2365\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1624\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1624\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2167\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2170\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1696\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1684\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2851\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2836\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2404\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2404\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1864\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2626\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2563\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2563\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3421\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3460\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1945\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1933\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2089\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2089\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2023\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2026\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2017\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2017\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2227\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2551\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2560\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2587\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2587\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2218\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1456\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1453\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1900\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1735\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1735\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2020\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2023\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2323\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2320\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2503\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2506\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1564\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1564\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1801\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1792\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2950\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2959\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3259\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3235\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1843\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1840\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1594\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1594\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2164\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2149\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2266\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2269\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3874\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3874\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3145\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3145\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2041\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2041\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2452\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2440\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1765\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1783\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2539\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2539\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1543\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2359\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2335\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1891\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1495\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1495\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2308\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2308\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1834\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1834\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2473\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2479\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2032\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2032\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3103\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3106\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2380\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2380\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2143\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2146\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2119\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2116\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1672\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1672\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2371\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2371\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1780\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1780\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2323\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2323\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1753\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1753\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2485\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2473\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1501\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1498\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3271\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3265\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2929\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2932\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2698\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2683\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2821\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2821\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2497\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2497\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1567\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1561\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1972\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1810\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1810\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2269\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1888\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2158\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1726\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1726\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2224\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2236\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2713\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2713\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3280\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3277\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2167\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2161\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2050\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1696\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1696\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2083\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2089\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1789\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1789\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2602\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2602\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3145\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3127\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1810\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1810\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1537\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1537\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1846\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2407\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2407\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2068\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2068\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2269\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2269\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3121\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3121\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2587\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2590\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2215\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2212\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2005\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2005\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2242\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2239\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3097\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3097\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1579\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1579\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2314\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2314\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1966\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3103\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3103\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1840\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1840\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1933\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3490\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3490\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1957\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1945\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1363\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1363\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1591\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1591\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1945\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2704\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2704\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1261\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1261\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3073\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3073\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1444\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1444\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1840\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1963\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1960\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1540\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1546\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1456\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1471\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1471\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2074\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2071\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1555\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1555\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1891\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 4204\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 4201\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1903\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1903\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1720\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1519\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1519\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2686\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2674\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1489\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1489\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1969\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2899\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2899\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3595\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3595\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1933\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1936\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1864\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1636\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1636\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2089\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2089\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2788\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2770\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2842\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2851\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2566\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2551\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1765\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3175\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3175\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2875\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2875\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1453\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1453\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1864\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1729\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1729\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2530\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2530\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1708\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1699\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1294\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1294\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2689\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2689\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2491\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2491\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2083\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2101\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2113\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2113\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1846\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1846\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2188\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3460\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3460\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1495\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1489\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2473\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2464\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2083\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2725\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2725\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3004\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3004\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1612\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1618\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1834\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2350\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2350\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2212\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2206\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2074\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2071\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2299\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2299\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2083\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2083\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3430\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3385\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2914\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2908\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2365\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2377\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1678\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1672\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1765\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1765\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1480\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1486\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2038\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2032\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2845\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2860\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1789\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1789\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2074\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2074\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2347\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2329\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1948\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1936\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1624\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1795\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1570\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2446\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2446\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1504\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1504\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3511\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3511\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2293\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2293\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2275\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2275\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2002\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2002\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1525\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1519\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2356\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2377\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2593\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2593\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2572\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2572\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2755\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2743\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1765\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1768\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2665\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2647\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2929\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2929\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1597\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1603\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1711\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1711\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2050\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2011\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2011\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2326\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2356\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1849\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2149\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2149\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1531\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1534\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1564\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1564\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1963\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1663\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1663\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2161\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2173\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2647\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2647\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3244\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3217\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2584\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2584\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2563\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2569\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1801\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1801\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2017\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2017\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2836\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2836\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1792\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1792\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1651\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1651\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 4051\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 4051\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2455\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2461\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1693\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1693\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1873\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1879\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1891\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2020\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2020\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2137\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2137\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2647\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2650\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1624\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1624\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1921\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1921\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1450\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1450\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2764\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2731\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2206\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2206\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2968\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2968\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1990\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1978\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1822\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2440\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2440\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1903\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1903\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2818\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2818\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2902\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2908\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2899\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2899\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1732\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1732\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2107\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2110\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1951\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1495\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1495\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2647\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2623\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1918\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1909\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2473\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2464\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2569\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2542\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1879\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1879\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3724\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3724\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2449\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2449\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2074\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2074\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1516\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1516\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2149\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1999\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1999\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1426\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1426\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2164\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2164\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1990\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2515\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2509\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2359\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2359\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1864\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1858\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1495\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1495\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1783\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1783\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2467\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2482\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2767\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2770\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2863\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2863\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2794\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2794\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3655\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3655\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1345\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1339\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1915\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1762\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1762\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2578\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2578\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2059\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2965\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2965\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2035\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2035\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2497\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2497\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1594\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1600\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1909\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1909\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2140\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2134\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1450\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2125\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1699\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1699\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1822\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1822\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2914\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2914\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2233\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2233\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2182\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2182\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2518\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2539\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1591\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1591\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3091\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3091\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2566\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2554\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2473\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2209\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2206\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2176\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2167\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2770\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2779\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2002\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2449\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2452\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2080\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2086\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2092\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1903\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3109\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3109\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2722\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2659\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2653\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2065\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1702\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1696\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1501\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1501\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1642\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2176\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2173\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2833\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2833\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 4216\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 4225\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 4033\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 4033\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1876\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1876\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2062\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2476\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2476\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2650\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2650\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1630\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1651\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3700\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3685\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1381\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1375\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1639\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2017\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2020\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2008\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2020\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2155\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1858\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1858\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1492\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1489\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1582\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1585\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2362\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2341\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2878\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2878\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2548\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2563\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 4912\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 4906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2152\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2158\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1750\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1747\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1513\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1510\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2074\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2692\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2716\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1660\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2017\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2017\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2020\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2020\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1768\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1768\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2041\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2041\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3190\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3190\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2500\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2497\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1810\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1819\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1816\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1816\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2281\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2275\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2269\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2275\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1369\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1369\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3193\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3193\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2155\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2155\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1753\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1756\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2671\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2704\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 3280\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3298\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1519\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1516\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1789\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1768\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1765\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1846\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1840\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2245\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2260\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 4324\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 4354\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2524\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2524\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2092\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2089\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2653\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2638\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2431\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2431\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2893\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2896\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1810\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1816\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1414\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1411\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2329\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2308\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2737\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2737\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2971\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2965\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2035\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2035\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1936\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1930\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2362\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2329\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1924\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1918\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2359\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2359\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2158\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2161\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2035\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2035\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2368\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2368\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1786\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1786\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2539\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2536\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1978\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1615\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1615\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2857\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1750\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1756\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1930\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2206\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3790\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3790\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1909\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1909\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2509\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2521\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2056\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2068\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1399\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1399\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2989\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2947\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2830\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2812\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2260\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2257\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2521\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2500\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1999\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2449\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2449\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2572\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2572\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1852\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1846\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2389\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2383\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2104\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2104\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1669\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1669\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1990\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1990\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1903\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1543\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1546\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2527\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2527\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1786\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1786\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1450\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1819\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1819\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2290\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1519\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1519\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1594\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1594\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1537\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1537\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1648\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1648\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2212\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3043\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3028\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2275\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2272\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2989\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2995\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2218\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2218\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2377\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2365\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1507\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1504\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2116\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2095\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3436\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3442\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1453\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1453\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1987\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3739\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3739\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2158\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2158\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2884\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2887\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1549\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1546\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1945\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1945\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1906\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2680\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2686\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1555\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1555\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2911\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2908\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1855\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3298\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3298\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2197\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2197\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2098\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2098\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1666\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1621\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1414\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1411\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2728\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2728\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2557\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2551\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2809\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1897\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2224\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2011\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2017\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2101\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2092\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2449\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2449\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2368\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2362\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1957\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1957\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1804\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1804\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1579\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1579\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2533\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2533\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2215\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1444\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1444\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2569\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2569\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1390\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1390\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2119\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2128\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1699\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2950\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 2953\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2926\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2926\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1624\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2026\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2026\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3178\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 3157\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2527\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2527\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1582\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1585\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2899\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2887\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2953\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2953\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1975\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2332\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2335\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2629\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2614\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1201\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2209\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2386\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2386\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1597\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1597\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1645\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1645\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1720\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1435\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1435\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2041\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2041\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1546\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1540\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3256\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3289\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1693\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1690\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1651\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1660\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1765\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1498\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1498\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1816\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1819\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1717\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2098\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2098\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1858\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1858\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2719\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2716\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1303\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1309\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1573\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1567\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1840\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1468\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1474\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2287\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2287\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1663\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1651\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1450\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1441\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2635\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2620\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3061\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3061\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2887\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2887\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1945\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1945\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1513\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1513\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2497\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2497\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2329\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2329\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1684\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1684\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2902\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2902\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1594\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1594\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2608\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3067\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3067\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1444\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1444\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3343\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3361\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2101\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2092\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2437\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1420\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1417\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1927\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2077\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2086\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3559\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3559\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2482\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2470\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3103\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3103\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2170\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2164\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1738\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1729\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1459\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1456\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1723\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2413\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2410\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1651\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3439\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3439\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1546\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1543\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1603\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1594\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1999\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1612\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1609\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2185\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1939\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1822\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1822\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2872\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2872\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2260\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2260\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2692\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2680\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2446\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2434\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1570\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1570\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1453\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1456\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2644\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2644\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1762\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1762\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1480\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1480\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1408\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1408\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2317\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2320\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1831\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1834\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1585\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1585\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2371\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2380\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1624\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1618\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1894\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2281\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2257\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1714\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1720\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1366\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1357\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2194\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1660\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1660\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2380\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2380\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2416\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2416\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2293\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2293\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2527\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1684\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1669\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3481\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 3481\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1834\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1831\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3445\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 3445\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2023\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2023\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2293\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2299\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1873\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1870\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2179\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2203\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2701\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2701\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2395\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2395\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1750\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1744\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2782\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2749\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2614\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2599\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2566\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2578\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1744\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2014\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2014\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 3850\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3832\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2614\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2626\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1984\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1981\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1696\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1696\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1726\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1726\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 2 / 9 \n", - "Reallocating..done. *alloclen = 1669\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1672\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1654\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1447\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1450\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1681\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1996\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1543\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2089\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2092\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1423\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1423\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1492\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1492\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1576\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1579\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2197\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2200\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1759\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2107\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2107\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1660\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1660\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2047\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 2053\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1576\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1582\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2848\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2866\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1882\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1669\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1669\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2221\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1675\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1675\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1879\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1885\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1861\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1867\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2407\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2407\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1825\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2533\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2551\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2674\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2674\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1645\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1633\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1708\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1708\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1675\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1675\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1522\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1813\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1813\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1483\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1483\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1828\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1837\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2500\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 2503\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1489\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1489\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1912\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 1903\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1657\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1660\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2500\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2500\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2827\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2851\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1864\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1864\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2779\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2776\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1747\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 1741\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2611\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1423\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1423\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3064\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 3064\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1627\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1993\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2182\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 4 / 9 \n", - "Reallocating..done. *alloclen = 2176\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2104\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2104\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 3 / 9 \n", - "Reallocating..done. *alloclen = 3268\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2014\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 2014\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2056\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2056\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 7 / 9 \n", - "Reallocating..done. *alloclen = 1816\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 8 / 9 \n", - "Reallocating..done. *alloclen = 1819\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1750\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 1750\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n", - "nthread = 0\n", - "nthreadpair = 0\n", - "nthreadtb = 0\n", - "ppenalty_ex = 0\n", - "stacksize: 8192 kb\n", - "generating a scoring matrix for nucleotide (dist=200) ... done\n", - "Gap Penalty = -1.53, +0.00, +0.00\n", - "\n", - "\n", - "\n", - "Making a distance matrix ..\n", - " 1 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=0) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 1/2... \n", - "STEP 5 / 9 \n", - "Reallocating..done. *alloclen = 2725\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "Making a distance matrix from msa.. \n", - " 0 / 10\n", - "done.\n", - "\n", - "Constructing a UPGMA tree (efffree=1) ... \n", - " 0 / 10\n", - "done.\n", - "\n", - "Progressive alignment 2/2... \n", - "STEP 6 / 9 \n", - "Reallocating..done. *alloclen = 2737\n", - "STEP 9 / 9 \n", - "done.\n", - "\n", - "disttbfast (nuc) Version 7.511\n", - "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n", - "0 thread(s)\n", - "\n", - "\n", - "Strategy:\n", - " FFT-NS-2 (Fast but rough)\n", - " Progressive method (guide trees were built 2 times.)\n", - "\n", - "If unsure which option to use, try 'mafft --auto input > output'.\n", - "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n", - "\n", - "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n", - "It tends to insert more gaps into gap-rich regions than previous versions.\n", - "To disable this change, add the --leavegappyregion option.\n", - "\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "652086\n", - "652086\n", - "652086\n", - "652086\n", - "652086\n", - "652086\n", - "652086\n", - "652086\n", - "652086\n", - "652086\n" - ] - } - ], - "source": [ - "import pandas as pd\n", - "import os\n", - "import numpy as np\n", - "import re\n", - "basedir=os.getcwd()\n", - "\n", - "for sp in ['synth_myco','synth_ecoli','synth_paeru']:\n", - " for frag in ['0.5','0.8','1']:\n", - " species=sp+'/'+frag+'/'\n", - " \n", - " comparisondir = basedir+'/'+species+'/Comparison' \n", - " CG_dir = comparisondir+'/GFs/CG'\n", - " cg_fa_panaroo = CG_dir+'/fasta_panaroo/'\n", - " msa_panaroo = CG_dir+'/msa_panaroo/'\n", - " os.makedirs(cg_fa_panaroo,exist_ok=True)\n", - " os.makedirs(msa_panaroo,exist_ok=True)\n", - "\n", - " prokkadir = basedir+'/'+species+'/Prokka' \n", - " panaroodir = basedir+'/'+species+'/Panaroo'\n", - " delosdir=basedir+'/'+species+'/PanDelos'\n", - "\n", - " # read in all gene sequences\n", - " gene2seq = dict()\n", - "\n", - " for file in os.listdir(prokkadir):\n", - " all_files = os.listdir(prokkadir+'/'+file)\n", - " ffn_file = [f for f in all_files if f.endswith('ffn')][0]\n", - " with open(prokkadir+'/'+file+'/'+ffn_file) as f:\n", - " lines=f.readlines()\n", - " gene=lines[0].split(' ')[0]\n", - " seq=''\n", - " for l in lines[1:]:\n", - " if l.startswith('>'):\n", - " gene2seq[gene]=seq\n", - " gene=l.split(' ')[0]\n", - " seq=''\n", - " else:\n", - " seq+=l.strip()\n", - " gene2seq[gene]=seq\n", - "\n", - " # create a dictionary mapping GFs to genes\n", - " itool = basedir+'/'+species+'Panaroo/gene_presence_absence.csv'\n", - " gf2genes=dict()\n", - " with open(itool,'r') as f:\n", - " lines = f.readlines()[1:] \n", - " for line in lines:\n", - " CG=True\n", - " name=line.split(',')[0]\n", - " cc = line.strip().split(',')[3:]\n", - " cc=[g for g in cc if g != '']\n", - " if len(cc)==10:\n", - " for c in cc:\n", - " if len(c.split(';'))>1 or len(c.split('_'))>2:\n", - " CG=False\n", - " if CG:\n", - " gf2genes[name]=cc\n", - " \n", - " # write to file one fasta for each (single-copy) core gene family\n", - " for gf in gf2genes: \n", - " genes=gf2genes[gf]\n", - "\n", - " with open(CG_dir+'/fasta_panaroo/'+gf+'.fa','w') as f:\n", - " for g in genes:\n", - " if '>'+g in gene2seq:\n", - " f.write('>'+g+'\\n')\n", - " f.write(str(gene2seq['>'+g])+'\\n') \n", - "\n", - " # Run Mafft\n", - " for f in os.listdir(cg_fa_panaroo):\n", - " ret=subprocess.call(['bash',basedir+\"/run_mafft.sh\",species,cg_fa_panaroo+f,msa_panaroo+f],stdout=subprocess.DEVNULL)\n", - "\n", - " # Concatenate alignments\n", - " genome2seqs=dict()\n", - " for file in os.listdir(msa_panaroo):\n", - " with open(msa_panaroo+file) as f:\n", - " lines=f.readlines()\n", - " genome=lines[0].split('_')[0]\n", - " seq=''\n", - " for l in lines[1:]:\n", - " if l.startswith('>'):\n", - "\n", - " if genome in genome2seqs:\n", - " genome2seqs[genome]=genome2seqs[genome]+seq \n", - " else:\n", - " genome2seqs[genome]=seq\n", - " seq=''\n", - " genome=l.split('_')[0]\n", - " else:\n", - " seq+=l.strip()\n", - " \n", - "\n", - " if genome in genome2seqs:\n", - " genome2seqs[genome]=genome2seqs[genome]+seq \n", - " else:\n", - " genome2seqs[genome]=seq\n", - "\n", - " # check all went well \n", - " for g in genome2seqs:\n", - " print(len(genome2seqs[g]))\n", - "\n", - " # Write to file a single concatenated alignment\n", - " with open(msa_panaroo+'concat.msa','w') as f:\n", - " for g in genome2seqs:\n", - " f.write(g+'\\n')\n", - " f.write(str(genome2seqs[g])+'\\n')\n", - "\n", - " # Build tree\n", - " ret=subprocess.call(['bash',basedir+\"/run_fasttree.sh\",species,msa_panaroo+'concat.msa',msa_panaroo+'concat.tree'],stdout=subprocess.DEVNULL)\n", - "\n", - " # Change names of genomes to correposnd to PANPROVA genomes\n", - " roary2genome = dict()\n", - " genome_names = os.listdir(delosdir+'/output/fragmented')\n", - " matchfile='predictedCDSs_filtered_only_genes.bed'\n", - " dict_list_names = [] \n", - " prokka_dirs=os.listdir(prokkadir)\n", - " for genome_full in prokka_dirs:\n", - " genome=genome_full.split('_')[2]\n", - " files=os.listdir(prokkadir+'/'+genome_full)\n", - " index_tsv = [i for i,name in enumerate(files) if re.search(\"tsv\", name)][0]\n", - "\n", - " with open(prokkadir+'/'+genome_full+'/'+files[index_tsv]) as f:\n", - " code=f.readlines()[1].split('\\t')[0].split('_')[0]\n", - " \n", - " roary2genome[code]=genome\n", - "\n", - " # Rename tree\n", - " with open(msa_panaroo+'concat.tree') as infile, open(msa_panaroo+'concat_renamed.tree', 'w') as outfile:\n", - " for line in infile:\n", - " for src, target in roary2genome.items():\n", - " line = line.replace(src, target)\n", - " outfile.write(line)\n" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "prog4bio", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:53) \n[GCC 9.4.0]" - }, - "orig_nbformat": 4, - "vscode": { - "interpreter": { - "hash": "6e0cb843de0f4fc4c56254867cd41133c4ad8e22d5fff20b7c7994166d38b73d" - } - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/synthetic_trees.py b/synthetic_trees.py new file mode 100644 index 0000000..0635d78 --- /dev/null +++ b/synthetic_trees.py @@ -0,0 +1,420 @@ +#!/usr/bin/python3 +import subprocess +import pandas as pd +import os +import re + +# Function used to read in PANPROVA GFs of complete genomes +# It returns a set of core gene families (represented as tuples) +def read_panprova_CG(species): + basedir=os.getcwd() + ipanprova = basedir+'/PANPROVA_'+species+'/1/survival_families' + + gf_cg_prova = set() + for line in open(ipanprova,'r'): + cc = line.strip().split(' ')[1:] + + genomes = set() + cc_filt=set() + for c in cc: + genome = c.split(',')[0].lstrip('(') + if genome not in genomes: + genomes.add(genome) + cc_filt.add((c)) + + size = len(genomes) + + # core GF + if size == 10: + gf_cg_prova.add(tuple(cc_filt)) + + return gf_cg_prova + + +# Function used to read in PanDelos GFs of complete genomes +# It returns a set of core gene families (represented as tuples) +def read_pandelos_CG(species, frag): + basedir=os.getcwd() + + species= species+'/'+frag + delosdir = basedir+'/'+species+'/PanDelos' + + with open(delosdir+"/output/output.clus") as f: + lines = f.readlines() + + cg_delos=set() + for l in lines: + l = l.rstrip() + l = l.split(' ') + genome_set = set() + selected_genes = [] + for gene in l: + genome = gene.split(':')[0] + if genome in genome_set: + continue + else: + genome_set.add(genome) + selected_genes.append(gene) + + if len(selected_genes)==10: + cg_delos.add(tuple(selected_genes)) + + return cg_delos + + +# Function used to read in GenAPI core gene families +# It returns a dictionary gene family 2 genes +def read_genapi_CG(species,frag): + basedir=os.getcwd() + species= species+'/'+frag + itool = basedir+'/'+species+'/GenAPI/clustered_genes_genapi.ffn.clstr' + gf2genes=dict() + with open(itool,'r') as f: + lines = f.readlines() + GF_name=lines[0].lstrip('>').split(' ')[1].rstrip() + GF_list=[] + genomes=set() + CG=False + + for l in lines[1:]: + if l.startswith('>'): + if len(GF_list) == 10 and CG == True: + gf2genes[GF_name]=GF_list + GF_name=l.lstrip('>').split(' ')[1].rstrip() + CG = True + genomes=set() + GF_list=[] + else: + gene= l.split('>')[1].split(':')[0] + genome=gene.split('_')[0] + if genome in genomes: + CG=False + genomes.add(genome) + GF_list.append(gene) + + return gf2genes + + +# Function used to read in Panaroo core gene families +# It returns a dictionary gene family 2 genes +def read_panaroo_CG(species,frag): + basedir=os.getcwd() + species= species+'/'+frag + itool = basedir+'/'+species+'Panaroo/gene_presence_absence.csv' + gf2genes=dict() + with open(itool,'r') as f: + lines = f.readlines()[1:] + for line in lines: + CG=True + name=line.split(',')[0] + cc = line.strip().split(',')[3:] + cc=[g for g in cc if g != ''] + if len(cc)==10: + for c in cc: + if len(c.split(';'))>1 or len(c.split('_'))>2: + CG=False + if CG: + gf2genes[name]=cc + + return gf2genes + + +# Function used to read in PANPROVA complete gene sequences +# It returns a dictionary gene name 2 sequence +def read_panprova_genes(species): + basedir=os.getcwd() + + # read all genes + gene2seq=dict() + ipanprova_blastdb = basedir+'/PANPROVA_'+species+'/1/blastdb/' + for file in os.listdir(ipanprova_blastdb): + if file.endswith('fna'): + with open(ipanprova_blastdb+'/'+file) as f: + lines = f.readlines() + for l in lines: + if l.startswith('>'): + gene_name = l[1:].rstrip() + else: + gene2seq[gene_name]=l.rstrip() + + return gene2seq + + +# Function used to read in PanDelos-frag gene sequences +# It returns a dictionary gene name 2 sequence +def read_pandelos_genes(species,frag): + basedir=os.getcwd() + species= species+'/'+frag + + delosdir = basedir+'/'+species+'/PanDelos' + + frag_dir = delosdir+'/output/fragmented_coordinates/' + records_pan = {} + for d in os.listdir(frag_dir): + with open(frag_dir+d+'/'+"coordinates_frag.sam") as f: + lines = f.readlines() + for l in lines: + if l.startswith('@'): + continue + l = l.split('\t') + name = l[0] + seq = l[9] + records_pan[name] = seq + return records_pan + +# Function used to read in GenAPI and Panaroo gene sequences (obtained from Prokka) +# It returns a dictionary gene name 2 sequence +def read_prokka_genes(species, frag): + basedir = os.getcwd() + species = species+'/'+frag + prokkadir = basedir+'/'+species+'/Prokka' + gene2seq = dict() + + for file in os.listdir(prokkadir): + all_files = os.listdir(prokkadir+'/'+file) + ffn_file = [f for f in all_files if f.endswith('ffn')][0] + with open(prokkadir+'/'+file+'/'+ffn_file) as f: + lines=f.readlines() + gene=lines[0].split(' ')[0] + seq='' + for l in lines[1:]: + if l.startswith('>'): + gene2seq[gene.lstrip('>')]=seq + gene=l.split(' ')[0] + seq='' + else: + seq+=l.strip() + gene2seq[gene.lstrip('>')]=seq + + return gene2seq + +# This function writes to fasta files the sequences of genes belonging to core gene families +# Each file represents a gene family. +def write_fasta_to_file(tool,gf_cg,gene2seq,species,frag): + basedir=os.getcwd() + CG_dir = basedir+'/'+species+'/'+frag+'/Comparison/CG' + + os.makedirs(CG_dir,exist_ok=True) + os.makedirs(CG_dir+'/fasta_'+tool,exist_ok=True) + + # write to file + i = 0 + for family in gf_cg: + with open(CG_dir+'/fasta_'+tool+'/fam_'+str(i)+'.fa','w') as f: + i += 1 + for gene in family: + f.write('>'+str(gene)+'\n') + f.write(str(gene2seq[gene])+'\n') + + +# Run Mafft on fasta files +def run_mafft(tool,species, frag): + basedir=os.getcwd() + CG_dir = basedir+'/'+species+'/'+frag+'/Comparison/CG' + + cg_fa = CG_dir+'/fasta_'+tool+'/' + msa = CG_dir+'/msa_'+tool+'/' + os.makedirs(msa,exist_ok=True) + + for f in os.listdir(CG_dir+'/fasta_'+tool+'/'): + if f not in os.listdir(CG_dir+'/msa_'+tool+'/'): + ret=subprocess.call(['bash',basedir+"/analysis_scripts/run_mafft.sh",species,cg_fa+f,msa+f],stdout=subprocess.DEVNULL) + +# Concatenate alignments of multiple gene families +def concatenate_alignments(tool,species, frag): + basedir=os.getcwd() + CG_dir = basedir+'/'+species+'/'+frag+'/Comparison/CG' + msa = CG_dir+'/msa_'+tool+'/' + + genome2seqs=dict() + for file in os.listdir(msa): + with open(msa+file) as f: + lines=f.readlines() + + if tool=='prova': + genome=lines[0].split(',')[0].lstrip('>(') + elif tool=='delos': + genome=lines[0].split(':')[0] + elif tool=='genapi' or tool=='panaroo': + genome=lines[0].split('_')[0] + + seq='' + for l in lines[1:]: + if l.startswith('>'): + + if genome in genome2seqs: + genome2seqs[genome]=genome2seqs[genome]+seq + else: + genome2seqs[genome]=seq + seq='' + + if tool=='prova': + genome=l.split(',')[0].lstrip('>(') + elif tool=='delos': + genome=l.split(':')[0] + elif tool=='genapi' or tool=='panaroo': + genome=l.split('_')[0] + + else: + seq+=l.strip() + + + if genome in genome2seqs: + genome2seqs[genome]=genome2seqs[genome]+seq + else: + genome2seqs[genome]=seq + + #check all went well + for g in genome2seqs: + print(len(genome2seqs[g])) + + return genome2seqs + +# Function used to map the genome names of the tools to those of PANPROVA +def translate_genome(tool,species, frag): + basedir = os.getcwd() + species = species+'/'+frag+'/' + # read pandelos file to associate pandelos aliases to genome name + if tool == 'delos': + delosdir = basedir+'/'+species+'/PanDelos' + + genome_names = os.listdir(delosdir+'/output/fragmented') + matchfile='predictedCDSs_filtered_only_genes.bed' + dict_list_names = [] + + for g in genome_names: + files = os.listdir(delosdir+'/output/fragmented/' + g + '/artifacts') + afile = [f for f in files if f.endswith(matchfile)][0] + with open(delosdir+'/output/fragmented/' + g + '/artifacts/' +afile) as f: + delos_name = f.readline().split('\t')[0] + + dict_row = {'genome':g, 'pandelos_name':delos_name} + dict_list_names.append(dict_row) + + names_df=pd.DataFrame(dict_list_names) + names_df + + delos2prova = dict() + for r in names_df.index: + delos2prova[names_df.loc[r,'pandelos_name']]=names_df.loc[r,'genome'] + + return delos2prova + else: + # Change names of genomes to correposnd to PANPROVA genomes + prokkadir= basedir+'/'+species+'/Prokka' + delosdir = basedir+'/'+species+'/PanDelos' + + roary2genome = dict() + genome_names = os.listdir(delosdir+'/output/fragmented') + matchfile='predictedCDSs_filtered_only_genes.bed' + dict_list_names = [] + prokka_dirs=os.listdir(prokkadir) + for genome_full in prokka_dirs: + genome=genome_full.split('_')[2] + files=os.listdir(prokkadir+'/'+genome_full) + index_tsv = [i for i,name in enumerate(files) if re.search("tsv", name)][0] + + with open(prokkadir+'/'+genome_full+'/'+files[index_tsv]) as f: + code=f.readlines()[1].split('\t')[0].split('_')[0] + + roary2genome[code]=genome + + return roary2genome + + +# Write to file concatenate alignments of multiple gene families +def concatenated_to_file(tool,species,frag,genome2seqs,translationdict=None): + basedir=os.getcwd() + CG_dir = basedir+'/'+species+'/'+frag+'/Comparison/CG' + msa = CG_dir+'/msa_'+tool+'/' + #write to file + with open(msa+'concat.msa','w') as f: + for g in genome2seqs: + if tool=='prova': + f.write('>'+g+'\n') + elif tool=='delos': + f.write('>'+translationdict[g.lstrip('>')].split('_')[1]+'\n') + elif tool=='genapi': + f.write('>'+translationdict[g.lstrip('>')]+'\n') + + f.write(str(genome2seqs[g])+'\n') + +# Build tree with FastTree +def build_tree(tool,species, frag): + basedir = os.getcwd() + CG_dir = basedir+'/'+species+'/'+frag+'/Comparison/CG' + msa = CG_dir+'/msa_'+tool+'/' + ret = subprocess.call(['bash',basedir+"/analysis_scripts/run_fasttree.sh",species,msa+'concat.msa',msa+'concat.tree'],stdout=subprocess.DEVNULL) + + +# Function to build tree and rename it on Roary core genes +def run_roary(species,frag): + basedir=os.getcwd() + species=species+'/'+frag + alndir = basedir+'/'+species+'/Roary/output/' # core gene alignment is already provided by Roary + ret=subprocess.call(['bash',basedir+"/analysis_scripts/run_fasttree.sh",species,alndir+'core_gene_alignment.aln',alndir+'core_gene_alignment.tree'],stdout=subprocess.DEVNULL) + + with open(alndir+'core_gene_alignment.tree') as infile, open(alndir+'core_gene_alignment_renamed.tree', 'w') as outfile: + for line in infile: + line = line.replace('prokka_genome_','') + line = line.replace('_fr.fasta','') + + outfile.write(line) + + +def main(): + basedir=os.getcwd() + for species in ['synth_myco','synth_ecoli','synth_paeru']: + # PANPROVA + gf_cg = read_panprova_CG(species) + gene2seq = read_panprova_genes(species) + write_fasta_to_file('prova',gf_cg, gene2seq,species,1) + run_mafft('prova',species, 1) + genome2seqs=concatenate_alignments('prova',species, 1) + concatenated_to_file('prova',species,frag,genome2seqs) + build_tree('prova',species, 1) + + for frag in ['0.5','0.8','1']: + # PanDelos-frags + gf_cg = read_pandelos_CG(species, frag) + gene2seq = read_pandelos_genes(species,frag) + write_fasta_to_file('delos',gf_cg, gene2seq,species,frag) + run_mafft('delos',species, frag) + concatenate_alignments('delos',species, frag) + genome2prova = translate_genome('delos',species,frag) + concatenated_to_file('delos',species,frag,genome2seqs,genome2prova) + build_tree('delos',species, frag) + + # Roary + run_roary(species, frag) # Roary already provides aligned core gene families, so only tree building is required + + # GenAPI + gf_cg = read_genapi_CG(species, frag) + gene2seq = read_prokka_genes(species,frag) + write_fasta_to_file('genapi',gf_cg, gene2seq,species,frag) + run_mafft('genapi',species, frag) + concatenate_alignments('genapi',species, frag) + genome2prova = translate_genome('genapi',species,frag) + concatenated_to_file('genapi',species,frag,genome2seqs,genome2prova) + build_tree('genapi',species, frag) + + # Panaroo + gf_cg = read_panaroo_CG(species, frag) + gene2seq = read_prokka_genes(species,frag) + write_fasta_to_file('panaroo',gf_cg, gene2seq,species,frag) + run_mafft('panaroo',species, frag) + concatenate_alignments('panaroo',species, frag) + genome2prova = translate_genome('panaroo',species,frag) + concatenated_to_file('panaroo',species,frag,genome2seqs,genome2prova) + build_tree('panaroo',species, frag) + + subprocess.call(['bash',basedir+"/analysis_scripts/run_ete3.sh"],stdout=subprocess.DEVNULL) + + # Show results + for species in ['synth_myco','synth_ecoli','synth_paeru']: + for frag in ['0.5','0.8','1']: + print(species+'/'+frag) + subprocess.call(['cat',basedir+'/'+species+'/'+frag+'/Comparison/ete3.log']) + +if __name__ == "__main__": + main() \ No newline at end of file diff --git a/tools_comparison.ipynb b/tools_comparison.ipynb index 4ee35fd..9fffe68 100644 --- a/tools_comparison.ipynb +++ b/tools_comparison.ipynb @@ -11,7 +11,7 @@ }, { "cell_type": "code", - "execution_count": 61, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -35,7 +35,7 @@ }, { "cell_type": "code", - "execution_count": 62, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ @@ -64,7 +64,7 @@ }, { "cell_type": "code", - "execution_count": 63, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ @@ -102,7 +102,7 @@ }, { "cell_type": "code", - "execution_count": 64, + "execution_count": 4, "metadata": {}, "outputs": [], "source": [ @@ -116,7 +116,7 @@ }, { "cell_type": "code", - "execution_count": 65, + "execution_count": 5, "metadata": {}, "outputs": [], "source": [ @@ -143,20 +143,22 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## 1)Synthetic data" + "## 1. Synthetic data" ] }, { "cell_type": "code", - "execution_count": 66, + "execution_count": 6, "metadata": {}, "outputs": [], "source": [ + "basedir = os.getcwd()\n", + "\n", "# For all fragmentation levels\n", "frags=['0.5','0.6','0.7','0.8','0.9','1']\n", "\n", "# This can be computed for all 3 species under analysis\n", - "species = 'synth_ecoli' # synth_myco synth_paeru" + "species = 'synth_paeru' # synth_myco synth_ecoli" ] }, { @@ -169,7 +171,7 @@ }, { "cell_type": "code", - "execution_count": 67, + "execution_count": 7, "metadata": {}, "outputs": [], "source": [ @@ -350,9 +352,48 @@ }, { "cell_type": "code", - "execution_count": 68, + "execution_count": 12, "metadata": {}, "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " PanDelos-frags GF Size Roary panaroo genapi PanProva\n", + "0 607 3 722 227 756 204\n", + "1 4597 1 19235 855 2354 1355\n", + "2 1236 2 1698 441 893 386\n", + "3 416 4 627 253 782 226\n", + "4 297 5 501 216 899 217\n", + "5 639 9 65 808 1264 620\n", + "6 1314 10 43 942 793 1386\n", + "7 268 6 472 221 945 209\n", + "8 396 8 175 397 1203 325\n", + "9 228 7 283 258 1063 195\n", + " PanDelos-frags GF Size Roary panaroo genapi PanProva\n", + "0 1425 2 2068 465 979 398\n", + "1 5316 1 22754 1019 2598 1457\n", + "2 715 3 849 227 823 216\n", + "3 434 4 684 261 906 222\n", + "4 305 5 670 209 1000 195\n", + "5 319 6 540 258 1108 231\n", + "6 422 8 213 424 1450 359\n", + "7 247 7 385 236 1317 205\n", + "8 709 9 82 880 1569 641\n", + "9 1775 10 55 1429 1094 1890\n", + " PanDelos-frags GF Size Roary panaroo genapi PanProva\n", + "0 5899 1 26333 1239 2692 1372\n", + "1 1627 2 2312 518 1088 483\n", + "2 460 4 814 241 998 212\n", + "3 828 3 987 247 925 240\n", + "4 336 5 746 208 1087 196\n", + "5 304 6 677 245 1251 221\n", + "6 266 7 426 247 1510 195\n", + "7 814 9 109 976 1915 679\n", + "8 404 8 270 405 1744 345\n", + "9 2263 10 75 1904 1406 2425\n" + ] + }, { "name": "stderr", "output_type": "stream", @@ -360,13 +401,65 @@ "/home/claudia/tools/anaconda3/envs/prog4bio/lib/python3.7/site-packages/IPython/core/interactiveshell.py:3552: DtypeWarning: Columns (8,9) have mixed types.Specify dtype option on import or set low_memory=False.\n", " exec(code_obj, self.user_global_ns, self.user_ns)\n" ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " PanDelos-frags GF Size Roary panaroo genapi PanProva\n", + "0 1666 2 2603 535 1125 269\n", + "1 6431 1 29799 1458 2518 1239\n", + "2 572 4 939 235 1158 285\n", + "3 955 3 1071 306 1127 260\n", + "4 347 5 912 204 1187 227\n", + "5 326 6 752 234 1396 231\n", + "6 2701 10 92 2393 1707 2888\n", + "7 908 9 127 1015 2241 766\n", + "8 440 8 310 420 2041 347\n", + "9 305 7 508 300 1715 226\n", + " PanDelos-frags GF Size Roary panaroo genapi PanProva\n", + "0 7138 1 33025 1665 2404 1281\n", + "1 1653 2 2952 330 902 132\n", + "2 847 3 1236 129 975 38\n", + "3 287 5 1015 218 1395 132\n", + "4 466 4 1067 157 1219 74\n", + "5 346 6 875 235 1664 206\n", + "6 357 7 618 325 2013 271\n", + "7 469 8 345 454 2338 397\n", + "8 958 9 160 1040 2630 761\n", + "9 3394 10 110 3069 2141 3652\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/claudia/tools/anaconda3/envs/prog4bio/lib/python3.7/site-packages/IPython/core/interactiveshell.py:3552: DtypeWarning: Columns (8,9) have mixed types.Specify dtype option on import or set low_memory=False.\n", + " exec(code_obj, self.user_global_ns, self.user_ns)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " PanDelos-frags GF Size Roary panaroo genapi PanProva\n", + "0 7909 1 35691 1836 2471 1357.0\n", + "1 1803 2 3046 261 845 149.0\n", + "2 916 3 1177 35 767 0.0\n", + "3 181 5 1136 18 1227 0.0\n", + "4 442 4 1105 24 990 0.0\n", + "5 159 6 1024 23 1526 0.0\n", + "6 104 7 775 53 2043 0.0\n", + "7 509 9 195 709 3254 157.0\n", + "8 153 8 479 185 2651 22.0\n", + "9 4997 10 163 4651 3213 5391.0\n" + ] } ], "source": [ "all_tools_l = []\n", "for fragmentation in frags:\n", " # set directories\n", - " basedir = os.getcwd()\n", " delosdir = basedir+'/'+species+'/'+fragmentation+'/PanDelos'\n", " roarydir = basedir+'/'+species+'/'+fragmentation+'/Roary'\n", "\n", @@ -397,6 +490,7 @@ " all_tools=all_tools.merge(genapi,on='GF Size',how='left')\n", " all_tools=all_tools.merge(prova,on='GF Size',how='left')\n", " all_tools=all_tools.fillna(0)\n", + " print(all_tools)\n", " all_tools_l.append(all_tools)" ] }, @@ -410,17 +504,17 @@ }, { "cell_type": "code", - "execution_count": 69, + "execution_count": 13, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "Absolute percentage difference of core genes in PanDelos-frags: 12.2\n", - "Absolute percentage difference of core genes in Roary: 98.5\n", - "Absolute percentage difference of core genes in panaroo: 36.8\n", - "Absolute percentage difference of core genes in genapi: 32.6\n" + "Absolute percentage difference of core genes in PanDelos-frags: 6.5\n", + "Absolute percentage difference of core genes in Roary: 96.9\n", + "Absolute percentage difference of core genes in panaroo: 20.8\n", + "Absolute percentage difference of core genes in genapi: 41.6\n" ] } ], @@ -462,21 +556,28 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 22, "metadata": {}, "outputs": [], "source": [ "# Extract gene sequences of genes that survived through fragmentation (partially or completely)\n", - "ret=subprocess.call(['bash',basedir+\"panprova_blast_scripts/run_extract_survival_genes.sh\",species],stdout=subprocess.DEVNULL)\n", - "\n", + "ret=subprocess.call(['bash',basedir+\"/panprova_blast_scripts/run_extract_survival_genes.sh\",species],stdout=subprocess.DEVNULL)" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [], + "source": [ "# BBH between complete gene sequences and fragmented gene sequences to identify correspondance between ground truth (PANPROVA) and tools\n", - "ret=subprocess.call(['bash',basedir+\"panprova_blast_scripts/run_blast_pandelos.sh\",species],stdout=subprocess.DEVNULL)\n", - "ret=subprocess.call(['bash',basedir+\"panprova_blast_scripts/run_blast_prokka.sh\",species],stdout=subprocess.DEVNULL)" + "ret=subprocess.call(['bash',basedir+\"/panprova_blast_scripts/run_blast_pandelos.sh\",species],stdout=subprocess.DEVNULL)\n", + "ret=subprocess.call(['bash',basedir+\"/panprova_blast_scripts/run_blast_prokka.sh\",species],stdout=subprocess.DEVNULL)" ] }, { "cell_type": "code", - "execution_count": 70, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -825,7 +926,7 @@ }, { "cell_type": "code", - "execution_count": 71, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -943,7 +1044,7 @@ }, { "cell_type": "code", - "execution_count": 72, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -994,7 +1095,7 @@ }, { "cell_type": "code", - "execution_count": 73, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -1054,7 +1155,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:53) \n[GCC 9.4.0]" + "version": "3.7.12" }, "orig_nbformat": 4, "vscode": {