diff --git a/HybPhyloMaker0a_preparedata.sh b/HybPhyloMaker0a_preparedata.sh
index ae8913d..a33fd3a 100644
--- a/HybPhyloMaker0a_preparedata.sh
+++ b/HybPhyloMaker0a_preparedata.sh
@@ -20,9 +20,9 @@
 
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
-# *                     Script 00a - Download & prepare data                     *
-# *                                   v.1.3.0                                    *
-# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
+# *                     Script 0a - Download & prepare data                      *
+# *                                   v.1.4.0                                    *
+# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * tomas.fer@natur.cuni.cz                                                      *
 # ********************************************************************************
 
diff --git a/HybPhyloMaker0b_preparereference.sh b/HybPhyloMaker0b_preparereference.sh
index a56957d..28641fb 100644
--- a/HybPhyloMaker0b_preparereference.sh
+++ b/HybPhyloMaker0b_preparereference.sh
@@ -19,8 +19,8 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                     Script 0b - Prepare pseudoreference                      *
-# *                                   v.1.3.1                                    *
-# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
+# *                                   v.1.4.0                                    *
+# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * tomas.fer@natur.cuni.cz                                                      *
 # ********************************************************************************
 
diff --git a/HybPhyloMaker0c_Rsetup_MetaCentrum.sh b/HybPhyloMaker0c_Rsetup_MetaCentrum.sh
index bd14ccb..5f83473 100644
--- a/HybPhyloMaker0c_Rsetup_MetaCentrum.sh
+++ b/HybPhyloMaker0c_Rsetup_MetaCentrum.sh
@@ -9,9 +9,9 @@
 
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
-# *                              Setup R packages                                *
-# *                                   v.1.3.1                                    *
-# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
+# *                 Script 0c - Setup R packages on Metacentrum                  *
+# *                                   v.1.4.0                                    *
+# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * tomas.fer@natur.cuni.cz                                                      *
 # ********************************************************************************
 
diff --git a/HybPhyloMaker1_rawprocess.sh b/HybPhyloMaker1_rawprocess.sh
index 725bb4a..4590b93 100644
--- a/HybPhyloMaker1_rawprocess.sh
+++ b/HybPhyloMaker1_rawprocess.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 #----------------MetaCentrum----------------
 #PBS -l walltime=1d
-#PBS -l nodes=1:ppn=1:debian8
+#PBS -l nodes=1:ppn=1:debian8:minspec=29
 #PBS -j oe
 #PBS -l mem=4gb
 #PBS -l scratch=80gb
@@ -20,8 +20,8 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                        Script 01 - Raw data processing                       *
-# *                                   v.1.3.3                                    *
-# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
+# *                                   v.1.4.0                                    *
+# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * tomas.fer@natur.cuni.cz                                                      *
 # * based on Weitemier et al. (2014), Applications in Plant Science 2(9): 1400042*
 # ********************************************************************************
diff --git a/HybPhyloMaker2_readmapping.sh b/HybPhyloMaker2_readmapping.sh
index 266e0c5..2ebb080 100644
--- a/HybPhyloMaker2_readmapping.sh
+++ b/HybPhyloMaker2_readmapping.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 #----------------MetaCentrum----------------
 #PBS -l walltime=2d
-#PBS -l nodes=1:ppn=4
+#PBS -l nodes=1:ppn=4:minspec=29
 #PBS -j oe
 #PBS -l mem=4gb
 #PBS -l scratch=80gb
@@ -20,8 +20,8 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                     Script 02 - Read mapping using bowtie2                   *
-# *                                   v.1.3.2                                    *
-# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
+# *                                   v.1.4.0                                    *
+# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * tomas.fer@natur.cuni.cz                                                      *
 # ********************************************************************************
 
@@ -43,6 +43,7 @@ if [[ $PBS_O_HOST == *".cz" ]]; then
 	module add samtools-1.3
 	module add perl-5.10.1
 	module add gcc-4.8.4
+	module add python34-modules-gcc
 	module add ococo-2016-11
 elif [[ $HOSTNAME == compute-*-*.local ]]; then
 	echo -e "\nHybPhyloMaker2 is running on Hydra...\n"
@@ -57,6 +58,7 @@ elif [[ $HOSTNAME == compute-*-*.local ]]; then
 	#Add necessary modules
 	module load bioinformatics/bowtie2/2.2.6
 	module load bioinformatics/samtools/1.3
+	module load bioinformatics/ococo/ #???
 else
 	echo -e "\nHybPhyloMaker2 is running locally...\n"
 	#settings for local run
@@ -222,19 +224,24 @@ for file in $(cat SamplesFileNames.txt); do
 		echo "Copying BAM..."
 		cp $path/$type/21mapped/${file}.bam .
 	fi
-	#CONSENSUS USING OCOCO
-	echo "Making consensus with OCOCO..."
-	ococo -i ${file}.bam -c $mincov -F ${file}.fasta 2>/dev/null
+	#CONSENSUS USING KINDEL/OCOCO
+	if [[ $conscall =~ "ococo" ]]; then
+		echo "Making consensus with OCOCO..."
+		ococo -i ${file}.bam -x ococo64 -c $mincov -F ${file}.fasta 2>/dev/null
+	else
+		echo "Making consensus with kindel..."
+		kindel -m $mincov -t $majthres ${file}.bam > ${file}.fasta
+	fi
 	#change name in fasta file
-	sed -i '1d' ${file}.fasta #delete first line
-	sed -i "1i >$file" ${file}.fasta #insert fasta header as a first line
+	sed -i.bak '1d' ${file}.fasta #delete first line
+	sed -i.bak "1i >$file" ${file}.fasta #insert fasta header as a first line
 	#Remove line breaks from fasta file
 	awk '!/^>/ { printf "%s", $0; n = "\n" } /^>/ { print n $0; n = "" } END { printf "%s", n }' ${file}.fasta > tmp && mv tmp ${file}.fasta
 	#put $nrns Ns to variable 'a' and $nrns ?s to variable 'b'
 	a=$(printf "%0.sN" $(seq 1 $nrns))
 	b=$(printf "%0.s?" $(seq 1 $nrns))
 	#replace all Ns separating exons by '?'
-	sed -i "s/$a/$b/g" ${file}.fasta
+	sed -i.bak "s/$a/$b/g" ${file}.fasta
 	#copy results to home
 	cp ${file}.fasta $path/$type/21mapped
 	#delete BAM
diff --git a/HybPhyloMaker3_generatepslx.sh b/HybPhyloMaker3_generatepslx.sh
index 7b2e478..9ad4e38 100644
--- a/HybPhyloMaker3_generatepslx.sh
+++ b/HybPhyloMaker3_generatepslx.sh
@@ -21,8 +21,8 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *         Script 03 - Process consensus after mapping, make pslx files         *
-# *                                   v.1.3.2                                    *
-# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
+# *                                   v.1.4.0                                    *
+# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * tomas.fer@natur.cuni.cz                                                      *
 # * based on Weitemier et al. (2014), Applications in Plant Science 2(9): 1400042*
 # ********************************************************************************
diff --git a/HybPhyloMaker4b_correctframe_translate.sh b/HybPhyloMaker4b_correctframe_translate.sh
new file mode 100644
index 0000000..1393649
--- /dev/null
+++ b/HybPhyloMaker4b_correctframe_translate.sh
@@ -0,0 +1,278 @@
+#!/bin/bash
+#PBS -l walltime=8h
+#PBS -l nodes=1:ppn=4:minspec=29
+#PBS -j oe
+#PBS -l mem=4gb
+#PBS -l scratch=4gb
+#PBS -N HybPhyloMaker4b_translate
+#PBS -m abe
+
+# ********************************************************************************
+# *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
+# *       Script 04b - Put exons to correct reading frame and translate          *
+# *                                   v.1.4.0                                    *
+# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
+# * tomas.fer@natur.cuni.cz                                                      *
+# ********************************************************************************
+
+
+#Take MAFFT exon alignment files, check for correct reading frame (+ remove incomplete triplets at the beginning and end of each exon)
+#and translate to amino acids using EMBOSS
+#Produce concatenation of
+#(1) corrected exonic nucleotide alignments (+ generate 2 partition files - by exons and by codon positions within exons)
+#(2) translated exons alignments
+
+#Complete path and set configuration for selected location
+if [[ $PBS_O_HOST == *".cz" ]]; then
+	echo -e "\nHybPhyloMaker-translate is running on MetaCentrum..."
+	#settings for MetaCentrum
+	#Copy file with settings from home and set variables from settings.cfg
+	cp -f $PBS_O_WORKDIR/settings.cfg .
+	. settings.cfg
+	. /packages/run/modules-2.0/init/bash
+	path=/storage/$server/home/$LOGNAME/$data
+	source=/storage/$server/home/$LOGNAME/HybSeqSource
+	othersourcepath=/storage/$server/home/$LOGNAME/$othersource
+	otherpslxpath=/storage/$server/home/$LOGNAME/$otherpslx
+	#Move to scratch
+	cd $SCRATCHDIR
+	#Add necessary modules
+	module add emboss-6.5.7
+	module add perl-5.10.1
+	module add python-3.4.1-gcc
+elif [[ $HOSTNAME == compute-*-*.local ]]; then
+	echo -e "\nHybPhyloMaker-translate is running on Hydra..."
+	#settings for Hydra
+	#set variables from settings.cfg
+	. settings.cfg
+	path=../$data
+	source=../HybSeqSource
+	othersourcepath=../$othersource
+	otherpslxpath=../$otherpslx
+	#Make and enter work directory
+	mkdir -p workdir04b
+	cd workdir04b
+	#Add necessary modules
+	module load bioinformatics/
+else
+	echo -e "\nHybPhyloMaker-translate is running locally..."
+	#settings for local run
+	#set variables from settings.cfg
+	. settings.cfg
+	path=../$data
+	source=../HybSeqSource
+	othersourcepath=../$othersource
+	otherpslxpath=../$otherpslx
+	#Make and enter work directory
+	mkdir -p workdir04b
+	cd workdir04b
+fi
+#Setting for the case when working with cpDNA
+if [[ $cp =~ "yes" ]]; then
+	echo -e "Working with cpDNA\n"
+	type="cp"
+else
+	echo -e "Working with exons\n"
+	type="exons"
+fi
+
+#Copy scripts
+cp $source/catfasta2phyml.pl .
+cp $source/AMAS.py .
+#Copy MAFFT exon alignments
+cp $path/$type/60mafft/*.mafft .
+#Make a dir for corrected exons and concatenated loci
+mkdir $path/$type/61mafft_corrected
+mkdir $path/$type/62mafft_translated
+mkdir $path/$type/80concatenated_exon_alignments_corrected
+mkdir $path/$type/90concatenated_exon_alignments_translated
+
+#Translate into frame 1, 2 and 3, count number of stop codons and save it to file
+echo -ne "Translating exons to all three reading frames and selecting the correct one..."
+ls *.mafft > listOfMAFFTFiles.txt
+for mafftfile in $(cat listOfMAFFTFiles.txt)
+do
+	#Replace gaps in sequences by 'n'
+	sed -i.bak '/>/!s/-/n/g' $mafftfile
+	echo $mafftfile >> ${mafftfile}_stopcodonnr_overview.txt
+	for i in 1 2 3
+	do
+		transeq fasta::$mafftfile -frame $i stdout | fgrep -o \* | wc -l >> stopcodonnr_${mafftfile}.txt
+	done
+	cat stopcodonnr_${mafftfile}.txt >> ${mafftfile}_stopcodonnr_overview.txt
+	cp ${mafftfile}_stopcodonnr_overview.txt $path/$type/62mafft_translated
+	#Select the frame with least number of stop codons
+	min=$(sort -n stopcodonnr_${mafftfile}.txt | head -1)
+	frame=$(grep -n ^${min}$ stopcodonnr_${mafftfile}.txt | cut -c1 | head -1)
+	#Generate modified DNA alignment (introduce frame shift)
+	#Number of added character is $frame-1 (i.e., frame1=0, frame2=1, frame3=2)
+	if [ "$frame" = 2 ]; then
+		add=2
+	elif [ "$frame" = 3 ]; then
+		add=1
+	elif [ "$frame" = 1 ]; then
+		add=0
+	fi
+	addcharacter=$(printf '%*s' $add '' | tr ' ' 'n')
+	#Add 'n's at the beginning of each nucleotide sequence (first remove line breaks from FASTA file - awk command, second add '???' after each line not beginning with '>' - sed command)
+	awk '!/^>/ { printf "%s", $0; n = "\n" } /^>/ { print n $0; n = "" } END { printf "%s", n }' ${mafftfile} |  sed '/>/!s/^/'"$addcharacter"'/' > ${mafftfile}.corrframe
+	#Add '???' at the end of each nucleotide sequence (i.e., after each line not beginning with '>')
+	#sed -i '/>/!s/$/???/' ${mafftfile}.corrframe
+	#Remove first three characters from sequences in case of frame shift to remove incomplete triplet
+	if [ "$frame" != 1 ]; then
+		sed -i.bak '/>/!s/^...//' ${mafftfile}.corrframe
+	fi
+	#Remove incomplete triplets from the end of exon (0, 1 or 2 bases)
+	#Compute length of the alignment (length of the first accession, i.e., second line)
+	len=$(cat ${mafftfile}.corrframe | head -2 | tail -1 | awk '{ print length }')
+	remove=`expr $len % 3` #Calculate modulo after division by 3, i.e., number of bases to be remove`
+	#Remove last 0, 1 or 2 characters from sequences (i.e., from each line not beginning with '>')
+	sed -i.bak '/>/!s/.\{'"$remove"'\}$//' ${mafftfile}.corrframe
+	#Copy corrected exon alignment to home
+	cp ${mafftfile}.corrframe $path/$type/61mafft_corrected
+	
+	#Translate corrected exon
+	transeq fasta::$mafftfile.corrframe -frame 1 -outseq ${mafftfile}.translated
+	#remove line breaks from translated FASTA file
+	awk '!/^>/ { printf "%s", $0; n = "\n" } /^>/ { print n $0; n = "" } END { printf "%s", n }' ${mafftfile}.translated > tmp && mv tmp ${mafftfile}.translated
+	#Add '???' at the end of each protein sequence (add '???' after each line not beginning with '>' - sed command)
+	#sed -i.bak '/>/!s/$/???/' ${mafftfile}.translated
+	#Remove last two characters from fasta headers (i.e., each line beginning with '>') - were introduced by EMBOSS transeq
+	sed -i.bak '/>/s/.\{2\}$//' ${mafftfile}.translated
+	#Copy translated exon alignment to home
+	cp ${mafftfile}.translated $path/$type/62mafft_translated
+done
+echo -e "done\n"
+
+echo -en "Preparing summary table..."
+#combine the information about stop codons by frame
+paste *overview.txt > stop_codons_by_frame.txt
+#transpose the matrix
+awk '
+{
+    for (i=1; i<=NF; i++)  {
+        a[NR,i] = $i
+    }
+}
+NF>p { p = NF }
+END {
+    for(j=1; j<=p; j++) {
+        str=a[1,j]
+        for(i=2; i<=NR; i++){
+            str=str" "a[i,j];
+        }
+        print str
+    }
+}' stop_codons_by_frame.txt > stop_codons_by_frame_transposed.txt
+awk '{print $1 }' stop_codons_by_frame_transposed.txt > names.txt
+awk '{print $2 " " $3 " " $4 }' stop_codons_by_frame_transposed.txt > stop_codons_by_frame.txt
+#put the lowest number as last column
+awk '{min=$1;for(i=1;i<=NF;i++){if($i < min) min = $i} print $0 " " min}' stop_codons_by_frame.txt > tmp && mv tmp stop_codons_by_frame.txt
+#put the number of zero stop codons as last column
+awk '{zeros=0;for(i=1;i<=NF-1;i++){if($i=="0") zeros++ } print $0 " " zeros }' stop_codons_by_frame.txt > tmp && mv tmp stop_codons_by_frame.txt
+#combine back with names
+paste names.txt stop_codons_by_frame.txt > tmp && mv tmp stop_codons_by_frame.txt
+cat stop_codons_by_frame.txt | tr " " "\t" > tmp && mv tmp stop_codons_by_frame.txt
+echo -e "done\n"
+
+#Filter exons
+echo -ne "Filtering exons..."
+#1. Remove exons with more than one reading frame with 0 stop codons
+awk '{if($6>1) print $1}' stop_codons_by_frame.txt > removed_more_than_1_possible_reading_frame.txt
+awk '{if($6<=1) print $0}' stop_codons_by_frame.txt > selected_exons.txt
+#2. Remove exons with lowest number of stop codons exceeding threshold (maxstop)
+awk -v val=$maxstop '{if($5>val) print $1}' stop_codons_by_frame.txt > removed_lowest_number_of_stop_codons_exceeded_maxstop.txt
+awk -v val=$maxstop '{if($5<=val) print $1}' selected_exons.txt > tmp && mv tmp selected_exons.txt
+#Copy lists to home
+cp selected_exons.txt $path/$type/62mafft_translated
+cp removed*.txt $path/$type/62mafft_translated
+
+#Modify translation summary and copy to home
+sed -i.bak 's/To_align_Assembly_//g' stop_codons_by_frame.txt
+sed -i.bak2 's/.fasta.mafft//g' stop_codons_by_frame.txt
+cp stop_codons_by_frame.txt $path/$type/62mafft_translated
+
+#Copy selected exons to folder
+mkdir selected
+mkdir selectedtranslated
+for i in $(cat selected_exons.txt); do
+	cp ${i}.translated selectedtranslated
+	cp ${i}.corrframe selected
+done
+
+#Modify selected exons (replace stopcodons by NNN)
+for i in $(cat selected_exons.txt); do
+	sed 's/.../&+/g;s/+$//' selected/${i}.corrframe | sed 's/taa/NNN/g' | sed 's/tag/NNN/g' | sed 's/tga/NNN/g' | sed 's/+//g' > selected/tmp && mv selected/tmp selected/${i}.corrframe
+	cp selected/${i}.corrframe $path/$type/61mafft_corrected
+done
+echo -e "done\n"
+#-----------------------CONCATENATE MODIFIED NUCLEOTIDE EXON ALIGNMENTS-----------------------
+echo -ne "Concatenating corrected exons..."
+#Modify mafft file names (from, i.e., To_align_Assembly_10372_Contig_1_516.fasta.mafft to To_align_Assembly_10372_*mafft)
+#(all files starting with "To_align_Assembly_10372_" will be merged)
+ls -1 selected/*.corrframe | cut -d'_' -f4 | sort -u | sed s/^/To_align_Assembly_/g | sed s/\$/_*mafft.corrframe/g > fileNamesForConcat.txt
+#Modify mafft file names - prepare names for saving concatenate alignments (not possible to use names above as they contain '*'), e.g. Assembly_10372
+ls -1 selected/*.corrframe | cut -d'_' -f4 | sort -u | sed s/^/CorrectedAssembly_/g > fileNamesForSaving.txt
+#Combine both files (make single file with two columns)
+paste fileNamesForConcat.txt fileNamesForSaving.txt > fileForLoop.txt
+
+#Concatenate the exon alignments (values from first and second column of fileForLoop.txt are assigned to variable 'a' and 'b', respectively),
+#transform fasta to phylip format, copy results from scratch to home
+cat fileForLoop.txt | while read -r a b; do
+	python3 AMAS.py concat -i selected/$a -f fasta -d dna -u fasta -t selected/${b}.fasta >/dev/null
+	python3 AMAS.py concat -i selected/$a -f fasta -d dna -u phylip -t selected/${b}.phylip >/dev/null
+	#Modify partition file for partitioning by codon positions
+	# cat partitions.txt			#take the file
+	# cut -d"_" -f2- 				#take 2nd and following parts of each line separated by "_" (remove 'p1_' etc. introduced by AMAS)
+	# awk '{ print $0 "\\3;" }'		#
+	# awk '{for(i=0;i<3;i++)print}'	#print each line 3-times
+	# awk -F '[=-]' '{ if (NR % 3 == 1) print $1 "_1=" $2 "-" $3; else if (NR % 3 == 2) print $1 "_2=" $2+1 "-" $3; else print $1 "_3=" $2+2 "-" $3}'
+	#								#set separators to '=' and '-' and on 1st, 2nd and 3rd line do different modifications (add _1, _2 or _3; leave unchanged, add 1 or add 2 to $2, i.e. start position)
+	# sed 's/-/ - /g'				#replace "-" by " - "
+	# sed 's/=/ = /g'				#replace "=" by " = "
+	cat partitions.txt | cut -d"_" -f2- | awk '{ print $0 "\\3;" }' | awk '{for(i=0;i<3;i++)print}' | awk -F '[=-]' '{ if (NR % 3 == 1) print $1 "_1=" $2 "-" $3; else if (NR % 3 == 2) print $1 "_2=" $2+1 "-" $3; else print $1 "_3=" $2+2 "-" $3}' | sed 's/-/ - /g' | sed 's/=/ = /g' | sed -e 's/^/DNA, /g' -e 's/To_align_//g' | sed 's/;//g' > selected/${b}.codonpart.file
+	#modify and rename partitions.txt
+	cat partitions.txt | cut -d"_" -f2- | sed -e 's/^/DNA, /g' -e 's/To_align_//g' > selected/${b}.part
+	#perl catfasta2phyml.pl -f $a > $b.fasta
+	#perl catfasta2phyml.pl $b.fasta > $b.phylip
+	#Copy concatenated alignments and partition files to home
+	cp selected/$b.* $path/$type/80concatenated_exon_alignments_corrected
+done
+echo -e "done\n"
+
+#-----------------------CONCATENATE TRANSLATED EXON ALIGNMENTS-----------------------
+echo -ne "Concatenating translated exons..."
+#Modify mafft file names (from, i.e., To_align_Assembly_10372_Contig_1_516.fasta.mafft.translated to To_align_Assembly_10372_*mafft.translated)
+#(all files starting with "To_align_Assembly_10372_" will be merged)
+ls -1 selectedtranslated/*.translated | cut -d'_' -f4 | sort -u | sed s/^/To_align_Assembly_/g | sed s/\$/_*mafft.translated/g > fileNamesForConcat.txt
+#Modify mafft file names - prepare names for saving concatenate alignments (not possible to use names above as they contain '*'), e.g. Assembly_10372
+ls -1 selectedtranslated/*.translated | cut -d'_' -f4 | sort -u | sed s/^/TranslatedAssembly_/g > fileNamesForSaving.txt
+#Combine both files (make single file with two columns)
+paste fileNamesForConcat.txt fileNamesForSaving.txt > fileForLoop.txt
+#Concatenate the exon alignments (values from first and second column of fileForLoop.txt are assigned to variable 'a' and 'b', respectively),
+#transform fasta to phylip format, copy results from scratch to home
+cat fileForLoop.txt | while read -r a b; do
+	python3 AMAS.py concat -i selectedtranslated/$a -f fasta -d aa -u fasta -t selectedtranslated/${b}.fasta >/dev/null
+	python3 AMAS.py concat -i selectedtranslated/$a -f fasta -d aa -u phylip -t selectedtranslated/${b}.phylip >/dev/null
+	#modify and rename partitions.txt
+	sed -i.bak -e 's/^/WAG, /g' -e 's/To_align_//g' partitions.txt
+	mv partitions.txt selectedtranslated/${b}.part
+	#perl catfasta2phyml.pl -f $a > $b.fasta
+	#perl catfasta2phyml.pl $b.fasta > $b.phylip
+	#Copy translated concatenated alignments to home
+	cp selectedtranslated/$b.* $path/$type/90concatenated_exon_alignments_translated
+done
+echo "done\n"
+
+#Clean scratch/work directory
+if [[ $PBS_O_HOST == *".cz" ]]; then
+	#delete scratch
+	if [[ ! $SCRATCHDIR == "" ]]; then
+		rm -rf $SCRATCHDIR/*
+	fi
+else
+	cd ..
+	rm -r workdir04b
+fi
+
+echo -e "\nScript HybPhyloMaker04b finished...\n"
\ No newline at end of file
diff --git a/HybPhyloMaker5_missingdataremoval.sh b/HybPhyloMaker5_missingdataremoval.sh
index ba4a8d4..d584469 100644
--- a/HybPhyloMaker5_missingdataremoval.sh
+++ b/HybPhyloMaker5_missingdataremoval.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 #----------------MetaCentrum----------------
 #PBS -l walltime=1d
-#PBS -l nodes=1:ppn=4
+#PBS -l nodes=1:ppn=4:minspec=29
 #PBS -j oe
 #PBS -l mem=12gb
 #PBS -l scratch=4gb
@@ -22,8 +22,8 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                      Script 05 - Missing data handling                       *
-# *                                   v.1.3.1                                    *
-# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
+# *                                   v.1.4.0                                    *
+# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * tomas.fer@natur.cuni.cz                                                      *
 # ********************************************************************************
 
@@ -96,6 +96,17 @@ else
 	type="exons"
 fi
 
+#Settings for (un)corrected reading frame
+if [[ $corrected =~ "yes" ]]; then
+	alnpath=$type/80concatenated_exon_alignments_corrected
+	alnpathselected=$type/81selected_corrected
+	treepath=$type/82trees_corrected
+else
+	alnpath=$type/70concatenated_exon_alignments
+	alnpathselected=$type/71selected
+	treepath=$type/72trees
+fi
+
 #Check necessary file
 echo -ne "Testing if input data are available..."
 if [[ $cp =~ "yes" ]]; then
@@ -113,36 +124,67 @@ if [[ $cp =~ "yes" ]]; then
 		exit 3
 	fi
 else
-	if [ -d "$path/$type/70concatenated_exon_alignments" ]; then
-		if [ "$(ls -A $path/$type/70concatenated_exon_alignments)" ]; then
-			echo -e "OK\n"
+	if [[ $corrected =~ "yes" ]]; then
+		if [ -d "$path/$type/80concatenated_exon_alignments_corrected" ]; then
+			if [ "$(ls -A $path/$type/80concatenated_exon_alignments_corrected)" ]; then
+				echo -e "OK\n"
+			else
+				echo -e "'$path/$type/80concatenated_exon_alignments_corrected' is empty. Exiting...\n"
+				rm -d ../workdir05/ 2>/dev/null
+				exit 3
+			fi
 		else
-			echo -e "'$path/$type/70concatenated_exon_alignments' is empty. Exiting...\n"
+			echo -e "'$path/$type/80concatenated_exon_alignments_corrected' is missing. Exiting...\n"
 			rm -d ../workdir05/ 2>/dev/null
 			exit 3
 		fi
 	else
-		echo -e "'$path/$type/70concatenated_exon_alignments' is missing. Exiting...\n"
-		rm -d ../workdir05/ 2>/dev/null
-		exit 3
+		if [ -d "$path/$type/70concatenated_exon_alignments" ]; then
+			if [ "$(ls -A $path/$type/70concatenated_exon_alignments)" ]; then
+				echo -e "OK\n"
+			else
+				echo -e "'$path/$type/70concatenated_exon_alignments' is empty. Exiting...\n"
+				rm -d ../workdir05/ 2>/dev/null
+				exit 3
+			fi
+		else
+			echo -e "'$path/$type/70concatenated_exon_alignments' is missing. Exiting...\n"
+			rm -d ../workdir05/ 2>/dev/null
+			exit 3
+		fi
 	fi
 fi
 
 #Test if folder for results exits
-if [ -d "$path/$type/71selected${MISSINGPERCENT}" ]; then
-	echo -e "Directory '$path/$type/71selected${MISSINGPERCENT}' already exists. Delete it or rename before running this script again. Exiting...\n"
-	rm -d ../workdir05/ 2>/dev/null
-	exit 3
+if [[ $corrected =~ "yes" ]]; then
+	if [ -d "$path/$type/81selected_corrected${MISSINGPERCENT}" ]; then
+		echo -e "Directory '$path/$type/81selected_corrected${MISSINGPERCENT}' already exists. Delete it or rename before running this script again. Exiting...\n"
+		rm -d ../workdir05/ 2>/dev/null
+		exit 3
+	else
+		if [[ ! $location == "1" ]]; then
+			if [ "$(ls -A ../workdir05)" ]; then
+				echo -e "Directory 'workdir05' already exists and is not empty. Delete it or rename before running this script again. Exiting...\n"
+				rm -d ../workdir05/ 2>/dev/null
+				exit 3
+			fi
+		fi
+	fi
 else
-	if [[ ! $location == "1" ]]; then
-		if [ "$(ls -A ../workdir05)" ]; then
-			echo -e "Directory 'workdir05' already exists and is not empty. Delete it or rename before running this script again. Exiting...\n"
-			rm -d ../workdir05/ 2>/dev/null
-			exit 3
+	if [ -d "$path/$type/71selected${MISSINGPERCENT}" ]; then
+		echo -e "Directory '$path/$type/71selected${MISSINGPERCENT}' already exists. Delete it or rename before running this script again. Exiting...\n"
+		rm -d ../workdir05/ 2>/dev/null
+		exit 3
+	else
+		if [[ ! $location == "1" ]]; then
+			if [ "$(ls -A ../workdir05)" ]; then
+				echo -e "Directory 'workdir05' already exists and is not empty. Delete it or rename before running this script again. Exiting...\n"
+				rm -d ../workdir05/ 2>/dev/null
+				exit 3
+			fi
 		fi
 	fi
 fi
-
 #Copy data folder to scratch
 if [[ $cp =~ "yes" ]]; then
 	cp $path/$type/60mafft/*.fasta .
@@ -151,15 +193,15 @@ if [[ $cp =~ "yes" ]]; then
 		# mv "$file" "${file%.fasta.mafft}.fasta"
 	# done
 else
-	cp $path/$type/70concatenated_exon_alignments/*.fasta .
+	cp $path/$alnpath/*.fasta .
 fi
 
 #-----------PREPARE ALIGNMENTS WITH SPECIES WITH MAXIMUM SPECIFIED MISSING DATA ONLY----------------------
 #Make a list of all fasta files
 ls *.fasta | cut -d"." -f1 > fileForDeletePercentage.txt
 #Make new dir for results
-mkdir $path/$type/71selected${MISSINGPERCENT}
-mkdir $path/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}
+mkdir $path/${alnpathselected}${MISSINGPERCENT}
+mkdir $path/${alnpathselected}${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}
 numberfiles=$(cat fileForDeletePercentage.txt | wc -l)
 calculating=0
 for file in $(cat fileForDeletePercentage.txt)
@@ -216,13 +258,13 @@ do
 	#sed -i.bak '/^>/{s/ /\n/}' ${file}_modif${MISSINGPERCENT}.fas
 	cat ${file}_modif${MISSINGPERCENT}.fas | tr " " "\n" > tmp && mv tmp ${file}_modif${MISSINGPERCENT}.fas
 	#Copy results home
-	cp ${file}_${MISSINGPERCENT}percN.fas $path/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}
-	cp ${file}_modif${MISSINGPERCENT}.fas $path/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}
+	cp ${file}_${MISSINGPERCENT}percN.fas $path/${alnpathselected}${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}
+	cp ${file}_modif${MISSINGPERCENT}.fas $path/${alnpathselected}${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}
 	calculating=$((calculating + 1))
 	echo -e "\t$file processed ($calculating out of $numberfiles)\n"
 done
 echo -e "\nDeleting samples with more than ${MISSINGPERCENT}% missing data finished."
-echo -e "Modified alignments saved in $path/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}"
+echo -e "Modified alignments saved in $path/${alnpathselected}${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}"
 
 #-----------MAKE A TABLE WITH % OF MISSING DATA IN EACH SPECIES AND ASSEMBLY----------------------
 #Prepare header file
@@ -236,7 +278,7 @@ awk '{_[FNR]=(_[FNR] OFS $2)}END{for (i=1; i<=FNR; i++) {sub(/^ /,"",_[i]); prin
 sed -i.bak '1s/^/species\n/' headers.txt
 #Combine headers and table with missing data
 paste headers.txt missing_percentage_overview.txt > missing_percentage_overview_and_headers.txt
-cp missing_percentage_overview_and_headers.txt $path/$type/71selected${MISSINGPERCENT}
+cp missing_percentage_overview_and_headers.txt $path/${alnpathselected}${MISSINGPERCENT}
 
 # Transpose data matrix (with percentages of missing data)
 awk '
@@ -285,7 +327,7 @@ sed -i '1s/ 0/ nr_assemblies_with_completely_missing_data/' transposedPlusMeanPl
 # Combine AssembliesList.txt and transposedPlusMeanPlusNumberOf100.txt
 paste AssembliesList.txt transposedPlusMeanPlusNumberOf100.txt > MissingDataOverview.txt
 # Copy table and list to home
-cp MissingDataOverview.txt $path/$type/71selected${MISSINGPERCENT}
+cp MissingDataOverview.txt $path/${alnpathselected}${MISSINGPERCENT}
 echo -e "Table with % of missing data per gene and sample saved to $path/$type/71selected${MISSINGPERCENT}\n"
 
 #-----------SELECTION OF MOST COMPLETE ASSEMBLIES----------------------
@@ -339,8 +381,8 @@ cat MissingDataOverview_${MISSINGPERCENT}.txt average_missing_${MISSINGPERCENT}.
 # Select assemblies with more than 75% of species (and delete first and last line including header and sum legend)
 awk -F' ' -v val=$SPECIESPRESENCE '( $(NF) > val/100 ) { print $1 }' MissingDataOverview_${MISSINGPERCENT}.txt | tail -n +2 | head -n -2 > selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt
 # Copy table and list to home
-cp MissingDataOverview_${MISSINGPERCENT}.txt $path/$type/71selected${MISSINGPERCENT}
-cp selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt $path/$type/71selected${MISSINGPERCENT}
+cp MissingDataOverview_${MISSINGPERCENT}.txt $path/${alnpathselected}${MISSINGPERCENT}
+cp selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt $path/${alnpathselected}${MISSINGPERCENT}
 echo -e "Assemblies including at least ${SPECIESPRESENCE}% of species selected"
 
 #-----------CALCULATE CHARACTERISTICS FOR ALL GENES AND FOR SELECTED GENES (USING AMAS)----------------------
@@ -397,8 +439,8 @@ else
 	R --slave -f alignmentSummary.R
 fi
 #Copy summary table to home
-cp summaryALL.txt $path/$type/71selected${MISSINGPERCENT}
-cp *.png $path/$type/71selected${MISSINGPERCENT}
+cp summaryALL.txt $path/${alnpathselected}${MISSINGPERCENT}
+cp *.png $path/${alnpathselected}${MISSINGPERCENT}
 rm summaryALL.txt
 rm *.png
 # 2. For selected genes
@@ -455,8 +497,8 @@ mv summaryALL.txt summarySELECTED_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt
 #Rename all PNG files generated by R (add '_${MISSINGPERCENT}_${SPECIESPRESENCE}')
 for file in *.png; do mv "$file" "${file/.png/_${MISSINGPERCENT}_${SPECIESPRESENCE}.png}"; done
 #Copy summary table and PNG files to home
-cp summarySELECTED_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt $path/$type/71selected${MISSINGPERCENT}
-cp *.png $path/$type/71selected${MISSINGPERCENT}
+cp summarySELECTED_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt $path/${alnpathselected}${MISSINGPERCENT}
+cp *.png $path/${alnpathselected}${MISSINGPERCENT}
 
 #Clean scratch/work directory
 if [[ $PBS_O_HOST == *".cz" ]]; then
diff --git a/HybPhyloMaker6a2_RAxML_trees_summary.sh b/HybPhyloMaker6a2_RAxML_trees_summary.sh
index f599ebd..0ebe34d 100644
--- a/HybPhyloMaker6a2_RAxML_trees_summary.sh
+++ b/HybPhyloMaker6a2_RAxML_trees_summary.sh
@@ -20,8 +20,8 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                  Script 06a2 - summary of RAxML gene trees                   *
-# *                                   v.1.3.1                                    *
-# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
+# *                                   v.1.4.0                                    *
+# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * tomas.fer@natur.cuni.cz                                                      *
 # ********************************************************************************
 
@@ -76,43 +76,54 @@ else
 	type="exons"
 fi
 
+#Settings for (un)corrected reading frame
+if [[ $corrected =~ "yes" ]]; then
+	alnpath=$type/80concatenated_exon_alignments_corrected
+	alnpathselected=$type/81selected_corrected
+	treepath=$type/82trees_corrected
+else
+	alnpath=$type/70concatenated_exon_alignments
+	alnpathselected=$type/71selected
+	treepath=$type/72trees
+fi
+
 #Check necessary file
 echo -ne "Testing if input data are available..."
-if [ -f "$path/$type/71selected${MISSINGPERCENT}/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt" ]; then
-	if [ -d "$path/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}" ]; then
-		if [ "$(ls -A $path/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT})" ]; then
-			if [ -d "$path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML" ]; then
-				if [ "$(ls -A $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML)" ]; then
+if [ -f "$path/${alnpathselected}${MISSINGPERCENT}/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt" ]; then
+	if [ -d "$path/${alnpathselected}${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}" ]; then
+		if [ "$(ls -A $path/${alnpathselected}${MISSINGPERCENT}/deleted_above${MISSINGPERCENT})" ]; then
+			if [ -d "$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML" ]; then
+				if [ "$(ls -A $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML)" ]; then
 					echo -e "OK\n"
 				else
-					echo -e "'$path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML' is empty. Exiting...\n"
+					echo -e "'$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML' is empty. Exiting...\n"
 					rm -d ../workdir06a2/ 2>/dev/null
 					exit 3
 				fi
 			else
-				echo -e "'$path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML' is missing. Exiting...\n"
+				echo -e "'$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML' is missing. Exiting...\n"
 				rm -d ../workdir06a2/ 2>/dev/null
 				exit 3
 			fi
 		else
-			echo -e "'$path/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}' is empty. Exiting...\n"
+			echo -e "'$path/${alnpathselected}${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}' is empty. Exiting...\n"
 			rm -d ../workdir06a2/ 2>/dev/null
 			exit 3
 		fi
 	else
-		echo -e "'$path/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}' is missing. Exiting...\n"
+		echo -e "'$path/${alnpathselected}${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}' is missing. Exiting...\n"
 		rm -d ../workdir06a2/ 2>/dev/null
 		exit 3
 	fi
 else
-	echo -e "'$path/$type/71selected${MISSINGPERCENT}/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt' is missing. Exiting...\n"
+	echo -e "'$path/${alnpathselected}${MISSINGPERCENT}/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt' is missing. Exiting...\n"
 	rm -d ../workdir06a2/ 2>/dev/null
 	exit 3
 fi
 
 #Test if folder for results exits
-if [ -f "$path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML/gene_properties.txt" ]; then
-	echo -e "File '$path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML/gene_properties.txt' already exists. You are probably going to owerwrite previous results. Delete this file or rename before running this script again. Exiting...\n"
+if [ -f "$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML/gene_properties.txt" ]; then
+	echo -e "File '$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML/gene_properties.txt' already exists. You are probably going to overwrite previous results. Delete this file or rename before running this script again. Exiting...\n"
 	rm -d ../workdir06a2/ 2>/dev/null
 	exit 3
 else
@@ -133,12 +144,12 @@ cp $source/LBscores.R .
 mkdir trees
 mkdir alignments
 #Copy all fasta alignments to subfolder 'alignments'
-cp $path/$type/71selected${MISSINGPERCENT}/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt .
+cp $path/${alnpathselected}${MISSINGPERCENT}/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt .
 for i in $(cat selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt); do
-	cp $path/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}/${i}_modif${MISSINGPERCENT}.fas alignments/
+	cp $path/${alnpathselected}${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}/${i}_modif${MISSINGPERCENT}.fas alignments/
 done
 #Copy all RAxML tree files (*.tre) with bootstrap values to subfolder 'trees'
-cp $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML/*bipartitions.Assembly* trees/
+cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML/*bipartitions.*Assembly* trees/
 #Rename RAxML trees
 cd trees
 for i in *; do
@@ -166,9 +177,9 @@ done
 for i in $(cat LBscores.csv | sed 1d | cut -d"," -f5 | sort | uniq); do
 	grep $i LBscores.csv | awk -F',' -v val=$i '{ if ($5 == val) result=$1 } END { print val "\t" result }' >> LBscoresSDPerLocus.txt
 done
-cp LBscores.csv $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
-cp LBscoresPerTaxon.txt $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
-cp LBscoresSDPerLocus.txt $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
+cp LBscores.csv $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
+cp LBscoresPerTaxon.txt $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
+cp LBscoresSDPerLocus.txt $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
 #Combine 'LBscoresSDPerLocus.txt' with 'tree_stats_table.csv'
 awk '{ print $2 }' LBscoresSDPerLocus.txt > tmp && mv tmp LBscoresSDPerLocus.txt
 paste tree_stats_table.csv LBscoresSDPerLocus.txt | tr "\t" "," > tmp && mv tmp tree_stats_table.csv
@@ -185,15 +196,15 @@ else
 fi
 
 #Copy results to home
-cp tree_stats_table.csv $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
-cp *.png $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
+cp tree_stats_table.csv $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
+cp *.png $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
 
 #----------------Combine tree summary table with alignment summary and print comparison plots----------------
 #Copy script
 cp $source/plotting_correlations.R .
 echo -e "Combining alignment and tree properties...\n"
 #Copy alignment summary
-cp $path/$type/71selected${MISSINGPERCENT}/summarySELECTED_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt .
+cp $path/${alnpathselected}${MISSINGPERCENT}/summarySELECTED_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt .
 #***Modify alignment summary***
 #Remove '_Assembly' (now locus names start with a number)
 sed -i.bak 's/Assembly_//g' summarySELECTED*.txt
@@ -237,13 +248,13 @@ if [[ $location == "1" ]]; then
 else
 	R --slave -f plotting_correlations.R >> R.log 2>&1
 fi
-cp genes_corrs.* $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
+cp genes_corrs.* $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
 rm genes_corrs.*
 mv combined.txt gene_properties.txt
-cp gene_properties.txt $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
+cp gene_properties.txt $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
 
 #Copy R.log to home
-cp R.log $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
+cp R.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
 
 #Clean scratch/work directory
 if [[ $PBS_O_HOST == *".cz" ]]; then
diff --git a/HybPhyloMaker6a_RAxML_for_selected.sh b/HybPhyloMaker6a_RAxML_for_selected.sh
index 578d6c1..3a6200c 100644
--- a/HybPhyloMaker6a_RAxML_for_selected.sh
+++ b/HybPhyloMaker6a_RAxML_for_selected.sh
@@ -20,8 +20,8 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                    Script 06a - RAxML gene tree building                     *
-# *                                   v.1.3.3                                    *
-# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2015 *
+# *                                   v.1.4.0                                    *
+# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * tomas.fer@natur.cuni.cz                                                      *
 # ********************************************************************************
 
@@ -77,31 +77,50 @@ else
 	type="exons"
 fi
 
+#Settings for (un)corrected reading frame
+if [[ $corrected =~ "yes" ]]; then
+	alnpath=$type/80concatenated_exon_alignments_corrected
+	alnpathselected=$type/81selected_corrected
+	treepath=$type/82trees_corrected
+else
+	alnpath=$type/70concatenated_exon_alignments
+	alnpathselected=$type/71selected
+	treepath=$type/72trees
+fi
+
+#Check compatible setting (corrected=no is incompatible with genepart=codon)
+if [[ $genetreepart == "codon" ]] && [[ $corrected == "no" ]]; then
+	echo "You have incompatible settings (partitioning by codon [genetreepart=codon] is not allowed with uncorrected data [corrected=no]."
+	echo "Change the settings before running the script again..."
+	rm -d ../workdir06a/ 2>/dev/null
+	exit 3
+fi
+
 #Check necessary file
 echo -ne "Testing if input data are available..."
-if [ -d "$path/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}" ]; then
-	if [ "$(ls -A $path/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT})" ]; then
-		if [ -f "$path/$type/71selected${MISSINGPERCENT}/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt" ]; then
+if [ -d "$path/$alnpathselected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}" ]; then
+	if [ "$(ls -A $path/$alnpathselected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT})" ]; then
+		if [ -f "$path/$alnpathselected${MISSINGPERCENT}/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt" ]; then
 			echo -e "OK\n"
 		else
-			echo -e "'$path/$type/71selected${MISSINGPERCENT}/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt' is missing. Exiting...\n"
+			echo -e "'$path/$alnpathselected${MISSINGPERCENT}/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt' is missing. Exiting...\n"
 			rm -d ../workdir06a/ 2>/dev/null
 			exit 3
 		fi
 	else
-		echo -e "'$path/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}' is empty. Exiting...\n"
+		echo -e "'$path/$alnpathselected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}' is empty. Exiting...\n"
 		rm -d ../workdir06a/ 2>/dev/null
 		exit 3
 	fi
 else
-	echo -e "'$path/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}' is missing. Exiting...\n"
+	echo -e "'$path/$alnpathselected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}' is missing. Exiting...\n"
 	rm -d ../workdir06a/ 2>/dev/null
 	exit 3
 fi
 
 #Test if folder for results exits
-if [ -d "$path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML" ]; then
-	echo -e "Directory '$path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML' already exists. Delete it or rename before running this script again. Exiting...\n"
+if [ -d "$path/$treepath${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML" ]; then
+	echo -e "Directory '$path/$treepath${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML' already exists. Delete it or rename before running this script again. Exiting...\n"
 	rm -d ../workdir06a/ 2>/dev/null
 	exit 3
 else
@@ -115,9 +134,9 @@ else
 fi
 
 #Add necessary scripts and files
-cp $path/$type/71selected${MISSINGPERCENT}/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt .
-mkdir -p $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}
-mkdir $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
+cp $path/${alnpathselected}${MISSINGPERCENT}/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt .
+mkdir -p $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}
+mkdir $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
 
 if [[ $location == "1" || $location == "2" ]]; then
 	echo -e "\nGenerating multiple jobs with $raxmlperjob alignments per job..."
@@ -125,7 +144,7 @@ if [[ $location == "1" || $location == "2" ]]; then
 	#Divide selected_genes$CUT.txt into files by $raxmlperjob
 	split --lines=$raxmlperjob selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.
 	rm selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt
-	cp selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.* $path/$type/71selected${MISSINGPERCENT}
+	cp selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.* $path/${alnpathselected}${MISSINGPERCENT}
 	for group in $(ls selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.*)
 	do
 		echo '#!/bin/bash' >> ${group}.sh
@@ -163,15 +182,30 @@ if [[ $location == "1" || $location == "2" ]]; then
 		echo 'MISSINGPERCENT='"$MISSINGPERCENT" >> ${group}.sh
 		echo 'SPECIESPRESENCE='"$SPECIESPRESENCE" >> ${group}.sh
 		echo 'type='"$type" >> ${group}.sh
+		echo 'corrected='"$corrected" >> ${group}.sh
 		echo 'location='"$location" >> ${group}.sh
 		echo 'genetreepart='"$genetreepart" >> ${group}.sh
 		echo 'raxmlpthreads='"$raxmlpthreads" >> ${group}.sh
-		echo 'cp '"$path"'/$type/71selected${MISSINGPERCENT}/'"$group"' .' >> ${group}.sh
+		echo 'if [[ $corrected =~ "yes" ]]; then' >> ${group}.sh
+		echo '  alnpath=$type/80concatenated_exon_alignments_corrected' >> ${group}.sh
+		echo '  alnpathselected=$type/81selected_corrected' >> ${group}.sh
+		echo '  treepath=$type/82trees_corrected' >> ${group}.sh
+		echo 'else' >> ${group}.sh
+		echo '  alnpath=$type/70concatenated_exon_alignments' >> ${group}.sh
+		echo '  alnpathselected=$type/71selected' >> ${group}.sh
+		echo '  treepath=$type/72trees' >> ${group}.sh
+		echo 'fi' >> ${group}.sh
+		echo 'cp '"$path"'/${alnpathselected}${MISSINGPERCENT}/'"$group"' .' >> ${group}.sh
 		echo 'cp '"$source"'/catfasta2phyml.pl .' >> ${group}.sh
 		echo 'for i in $(cat '"$group"')' >> ${group}.sh
 		echo 'do' >> ${group}.sh
-		echo '  cp '"$path"'/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}/${i}_modif${MISSINGPERCENT}.fas .' >> ${group}.sh
-		echo '  cp $path/$type/70concatenated_exon_alignments/${i}.part .' >> ${group}.sh
+		echo '  cp '"$path"'/${alnpathselected}${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}/${i}_modif${MISSINGPERCENT}.fas .' >> ${group}.sh
+		echo '  if [[ $genetreepart == "exon" ]]; then' >> ${group}.sh
+		echo '    cp $path/${alnpath}/${i}.part .' >> ${group}.sh
+		echo '  elif [[ $genetreepart == "codon" ]]; then' >> ${group}.sh
+		echo '    cp $path/${alnpath}/${i}.codonpart.file .' >> ${group}.sh
+		echo '    mv ${i}.codonpart.file ${i}.part' >> ${group}.sh
+		echo '  fi' >> ${group}.sh
 		echo '  #Substitute '"'('"' by '"'_'"' and '"')'"' by nothing ('"'('"' and '"')'"' not allowed in RAxML)' >> ${group}.sh
 		echo '  sed -i '"'s/(/_/g'"' ${i}_modif${MISSINGPERCENT}.fas' >> ${group}.sh
 		echo '  sed -i '"'s/)//g'"' ${i}_modif${MISSINGPERCENT}.fas' >> ${group}.sh
@@ -186,20 +220,43 @@ if [[ $location == "1" || $location == "2" ]]; then
 		echo '  #modify name for partition file (remove '_modif${MISSINGPERCENT}')' >> ${group}.sh
 		echo '  filepart=$(sed "s/_modif${MISSINGPERCENT}//" <<< $file)' >> ${group}.sh
 		echo '  #RAxML with 100 rapid bootstrap' >> ${group}.sh
-		echo '  if [[ $location == "1" ]]; then' >> ${group}.sh
-		echo '    if [[ $genetreepart == "yes" ]]; then' >> ${group}.sh
-		echo '      raxmlHPC-PTHREADS -T $TORQUE_RESC_TOTAL_PROCS -f a -s $file.phylip -q $filepart.part -n $file.result -m GTRCAT -p 1234 -x 1234 -N 100' >> ${group}.sh
+		echo '  #1.Check if there are completely undetermined columns in alignment (RAxML -y will produced .reduced alignment and partition files)' >> ${group}.sh
+		echo '  #  Compute parsimony tree only and produce reduced alignment and appropriate reduced partition file' >> ${group}.sh
+		echo '  if [[ $genetreepart == "no" ]]; then' >> ${group}.sh
+		echo '    $raxmlseq -y -m GTRCAT -p 12345 -s $file.fas -n $file.check >> raxml.log' >> ${group}.sh
+		echo '  else' >> ${group}.sh
+		echo '    $raxmlseq -y -m GTRCAT -p 12345 -s $file.fas -q $filepart.part -n $file.check >> raxml.log' >> ${group}.sh
+		echo '  fi' >> ${group}.sh
+		echo '  #2.Test if reduced files were produced' >> ${group}.sh
+		echo '  if [ -f $file.fas.reduced ]; then' >> ${group}.sh
+		echo '    echo "Reduced alignment found...using it" >> raxml.log' >> ${group}.sh
+		echo '    if [[ $genetreepart == "no" ]]; then' >> ${group}.sh
+		echo '      rm $file.fas' >> ${group}.sh
+		echo '      mv $file.fas.reduced $file.fas' >> ${group}.sh
 		echo '    else' >> ${group}.sh
+		echo '      rm $filepart.part' >> ${group}.sh
+		echo '      mv $filepart.part.reduced $filepart.part' >> ${group}.sh
+		echo '      rm $file.fas' >> ${group}.sh
+		echo '      mv $file.fas.reduced $file.fas' >> ${group}.sh
+		echo '    fi' >> ${group}.sh
+		echo '  else' >> ${group}.sh
+		echo '    echo "Reduced alignment not found...using original alignment" >> raxml.log' >> ${group}.sh
+		echo '  fi' >> ${group}.sh
+		echo '  #3.Run RAxML' >> ${group}.sh
+		echo '  if [[ $location == "1" ]]; then' >> ${group}.sh
+		echo '    if [[ $genetreepart == "no" ]]; then' >> ${group}.sh
 		echo '      raxmlHPC-PTHREADS -T $TORQUE_RESC_TOTAL_PROCS -f a -s $file.phylip -n $file.result -m GTRCAT -p 1234 -x 1234 -N 100' >> ${group}.sh
+		echo '    else' >> ${group}.sh
+		echo '      raxmlHPC-PTHREADS -T $TORQUE_RESC_TOTAL_PROCS -f a -s $file.phylip -q $filepart.part -n $file.result -m GTRCAT -p 1234 -x 1234 -N 100' >> ${group}.sh
 		echo '    fi'  >> ${group}.sh
 		echo '  elif [[ $location == "2" ]]; then' >> ${group}.sh
-		echo '    if [[ $genetreepart == "yes" ]]; then' >> ${group}.sh
-		echo '      $raxmlpthreads -T $NSLOTS -f a -s $file.phylip -q $filepart.part -n $file.result -m GTRCAT -p 1234 -x 1234 -N 100' >> ${group}.sh
-		echo '    else' >> ${group}.sh
+		echo '    if [[ $genetreepart == "no" ]]; then' >> ${group}.sh
 		echo '      $raxmlpthreads -T $NSLOTS -f a -s $file.phylip -n $file.result -m GTRCAT -p 1234 -x 1234 -N 100' >> ${group}.sh
+		echo '    else' >> ${group}.sh
+		echo '      $raxmlpthreads -T $NSLOTS -f a -s $file.phylip -q $filepart.part -n $file.result -m GTRCAT -p 1234 -x 1234 -N 100' >> ${group}.sh
 		echo '    fi'  >> ${group}.sh
 		echo '  fi' >> ${group}.sh
-		echo '  cp *$file.result '"$path"'/$type/72trees'"${MISSINGPERCENT}_${SPECIESPRESENCE}"'/RAxML' >> ${group}.sh
+		echo '  cp *$file.result '"${path}/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}"'/RAxML' >> ${group}.sh
 		echo 'done' >> ${group}.sh
 		echo '#Clean scratch/work directory' >> ${group}.sh
 		echo 'if [[ $PBS_O_HOST == *".cz" ]]; then' >> ${group}.sh
@@ -212,10 +269,10 @@ if [[ $location == "1" || $location == "2" ]]; then
 		
 		chmod +x ${group}.sh
 		if [[ $location == "1" ]]; then
-			cp ${group}.sh $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
+			cp ${group}.sh $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
 			qsub ${group}.sh
 		else
-			cp ${group}.sh $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
+			cp ${group}.sh $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
 			cp ${group}.sh ..
 			echo 'qsub '"${group}"'.sh' >> ../submitRAxMLjobs.sh
 		fi
@@ -227,8 +284,13 @@ else
 	echo -e "Modifying selected FASTA files...\n"
 	for i in $(cat selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt)
 	do
-		cp $path/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}/${i}_modif${MISSINGPERCENT}.fas .
-		cp $path/$type/70concatenated_exon_alignments/${i}.part .
+		cp $path/${alnpathselected}${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}/${i}_modif${MISSINGPERCENT}.fas .
+		if [[ $genetreepart == "exon" ]]; then
+			cp $path/${alnpath}/${i}.part .
+		elif [[ $genetreepart == "codon" ]]; then
+			cp $path/${alnpath}/${i}.codonpart.file .
+			mv ${i}.codonpart.file ${i}.part
+		fi
 		#Substitute '(' by '_' and ')' by nothing ('(' and ')' not allowed in RAxML)
 		sed -i.bak 's/(/_/g' ${i}_modif${MISSINGPERCENT}.fas
 		sed -i.bak 's/)//g' ${i}_modif${MISSINGPERCENT}.fas
@@ -248,15 +310,38 @@ else
 		#modify name for partition file (remove '_modif${MISSINGPERCENT}'
 		filepart=$(sed "s/_modif${MISSINGPERCENT}//" <<< $file)
 		#run RAxML
+		#1.Check if there are completely undetermined columns in alignment (RAxML -y will produced .reduced alignment and partition files)
+		#  Compute parsimony tree only and produce reduced alignment and appropriate reduced partition file
+		if [[ $genetreepart == "no" ]]; then
+			$raxmlseq -y -m GTRCAT -p 12345 -s $file.fas -n $file.check >> raxml.log
+		else
+			$raxmlseq -y -m GTRCAT -p 12345 -s $file.fas -q $filepart.part -n $file.check >> raxml.log
+		fi
+		#2.Test if reduced files were produced
+		if [ -f $file.fas.reduced ]; then
+			echo "Reduced alignment found...using it" >> raxml.log
+			if [[ $genetreepart == "no" ]]; then
+				rm $file.fas
+				mv $file.fas.reduced $file.fas
+			else
+				rm $filepart.part
+				mv $filepart.part.reduced $filepart.part
+				rm $file.fas
+				mv $file.fas.reduced $file.fas
+			fi
+		else
+			echo "Reduced alignment not found...using original alignment" >> raxml.log
+		fi
+		#3.Run RAxML
 		if [[ $genetreepart == "yes" ]]; then
-			$raxmlpthreads -T $numbcores -f a -s $file.fas -q $filepart.part -n $file.result -m GTRCAT -p 1234 -x 1234 -N 100 >> raxml.log
+			$raxmlpthreads -T $numbcores -f a -s $file.fas -n $file.result -m GTRCAT -p 1234 -x 1234 -N 100 >> raxml.log
 		else
-			$raxmlpthreads -T $numbcores -f a -s $file.fas -q -n $file.result -m GTRCAT -p 1234 -x 1234 -N 100 >> raxml.log
+			$raxmlpthreads -T $numbcores -f a -s $file.fas -q $filepart.part -n $file.result -m GTRCAT -p 1234 -x 1234 -N 100 >> raxml.log
 		fi
-		cp *$file.result $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
+		cp *${file}.result $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
 	done
 #Copy raxml.log to home
-cp raxml.log $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
+cp raxml.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML
 fi
 
 #Clean scratch/work directory
@@ -275,5 +360,6 @@ if [[ $location == "2" ]]; then
 	echo -e "\nGo to homedir and run submitRAxMLjobs.sh..."
 elif [[ $location == "1" ]]; then
 	echo -e "\nAfter all jobs finish run script HybPhyloMaker6a2 in order to calculate tree properties..."
+elif [[ $location == "0" ]]; then
+	echo -e "\nRun script HybPhyloMaker6a2 in order to calculate tree properties..."
 fi
-echo -e "\nRun script HybPhyloMaker6a2 in order to calculate tree properties..."
diff --git a/HybPhyloMaker6b_FastTree_for_selected.sh b/HybPhyloMaker6b_FastTree_for_selected.sh
index cac1c9c..cd1d039 100644
--- a/HybPhyloMaker6b_FastTree_for_selected.sh
+++ b/HybPhyloMaker6b_FastTree_for_selected.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 #----------------MetaCentrum----------------
 #PBS -l walltime=1d
-#PBS -l nodes=1:ppn=4
+#PBS -l nodes=1:ppn=4:minspec=29
 #PBS -j oe
 #PBS -l mem=16gb
 #PBS -l scratch=4gb
@@ -21,8 +21,8 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                   Script 06b - FastTree gene tree building                   *
-# *                                   v.1.3.1                                    *
-# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
+# *                                   v.1.4.0                                    *
+# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * tomas.fer@natur.cuni.cz                                                      *
 # ********************************************************************************
 
@@ -86,31 +86,42 @@ else
 	type="exons"
 fi
 
+#Settings for (un)corrected reading frame
+if [[ $corrected =~ "yes" ]]; then
+	alnpath=$type/80concatenated_exon_alignments_corrected
+	alnpathselected=$type/81selected_corrected
+	treepath=$type/82trees_corrected
+else
+	alnpath=$type/70concatenated_exon_alignments
+	alnpathselected=$type/71selected
+	treepath=$type/72trees
+fi
+
 #Check necessary file
 echo -ne "Testing if input data are available..."
-if [ -f "$path/$type/71selected${MISSINGPERCENT}/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt" ]; then
-	if [ -d "$path/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}" ]; then
-		if [ "$(ls -A $path/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT})" ]; then
+if [ -f "$path/${alnpathselected}${MISSINGPERCENT}/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt" ]; then
+	if [ -d "$path/${alnpathselected}${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}" ]; then
+		if [ "$(ls -A $path/${alnpathselected}${MISSINGPERCENT}/deleted_above${MISSINGPERCENT})" ]; then
 			echo -e "OK\n"
 		else
-			echo -e "'$path/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}' is empty. Exiting...\n"
+			echo -e "'$path/${alnpathselected}${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}' is empty. Exiting...\n"
 			rm -d ../workdir06b/ 2>/dev/null
 			exit 3
 		fi
 	else
-		echo -e "'$path/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}' is missing. Exiting...\n"
+		echo -e "'$path/${alnpathselected}${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}' is missing. Exiting...\n"
 		rm -d ../workdir06b/ 2>/dev/null
 		exit 3
 	fi
 else
-	echo -e "'$path/$type/71selected${MISSINGPERCENT}/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt' is missing. Exiting...\n"
+	echo -e "'$path/${alnpathselected}${MISSINGPERCENT}/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt' is missing. Exiting...\n"
 	rm -d ../workdir06b/ 2>/dev/null
 	exit 3
 fi
 
 #Test if folder for results exits
-if [ -d "$path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree" ]; then
-	echo -e "Directory '$path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree' already exists. Delete it or rename before running this script again. Exiting...\n"
+if [ -d "$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree" ]; then
+	echo -e "Directory '$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree' already exists. Delete it or rename before running this script again. Exiting...\n"
 	rm -d ../workdir06b/ 2>/dev/null
 	exit 3
 else
@@ -129,12 +140,12 @@ cp $source/catfasta2phyml.pl .
 cp $source/AMAS.py .
 cp $source/CompareToBootstrap.pl .
 cp $source/MOTree.pm .
-cp $path/$type/71selected${MISSINGPERCENT}/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt .
+cp $path/${alnpathselected}${MISSINGPERCENT}/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt .
 # Copy and modify selected FASTA files
 echo -en "\nModifying selected FASTA files..."
 for i in $(cat selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt)
 do
-	cp $path/$type/71selected${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}/${i}_modif${MISSINGPERCENT}.fas .
+	cp $path/${alnpathselected}${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}/${i}_modif${MISSINGPERCENT}.fas .
 	#Substitute '(' by '_' and ')' by nothing ('(' and ')' not allowed in FastTree)
 	sed -i.bak 's/(/_/g' ${i}_modif${MISSINGPERCENT}.fas
 	sed -i.bak 's/)//g' ${i}_modif${MISSINGPERCENT}.fas
@@ -145,8 +156,8 @@ done
 #Make a list of all fasta files
 ls *.fas | cut -d"." -f1 > FileForFastTree.txt
 #Make dir for results
-mkdir -p $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}
-mkdir -p $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+mkdir -p $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}
+mkdir -p $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
 
 echo -e "done\n"
 #----------------Generate gene trees using FastTree----------------
@@ -165,10 +176,10 @@ for file in $(cat FileForFastTree.txt); do
 	else
 		$fasttreebin -nt ${file}.fas > ${file}.fast.tre 2>>FastTree.log
 	fi
-	cp *$file.fast.tre $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+	cp *$file.fast.tre $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
 done
 #Copy log to home
-cp FastTree.log $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+cp FastTree.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
 
 #----------------Generate bootstrapped gene trees using FastTree----------------
 #Bootstrap using FastTree 
@@ -229,11 +240,11 @@ if [[ $FastTreeBoot =~ "yes" ]]; then
 		#Map bootstrap support values onto the original tree
 		perl ./CompareToBootstrap.pl -tree *${file}.fast.tre -boot ${file}.boot.fast.trees > ${file}.boot.fast.tre
 		#Copy bootstrap trees and final tree with bootstrap values to home
-		cp ${file}.boot.fast.trees $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
-		cp ${file}.boot.fast.tre $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+		cp ${file}.boot.fast.trees $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+		cp ${file}.boot.fast.tre $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
 	done
 	#Copy logs to home
-	cp *.log $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+	cp *.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
 fi
 
 #----------------Make a summary table with statistical properties for trees using R----------------
@@ -266,9 +277,9 @@ done
 for i in $(cat LBscores.csv | sed 1d | cut -d"," -f5 | sort | uniq); do
 	grep $i LBscores.csv | awk -F',' -v val=$i '{ if ($5 == val) result=$1 } END { print val "\t" result }' >> LBscoresSDPerLocus.txt
 done
-cp LBscores.csv $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
-cp LBscoresPerTaxon.txt $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
-cp LBscoresSDPerLocus.txt $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+cp LBscores.csv $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+cp LBscoresPerTaxon.txt $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+cp LBscoresSDPerLocus.txt $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
 #Combine 'LBscoresSDPerLocus.txt' with 'tree_stats_table.csv'
 awk '{ print $2 }' LBscoresSDPerLocus.txt > tmp && mv tmp LBscoresSDPerLocus.txt
 paste tree_stats_table.csv LBscoresSDPerLocus.txt | tr "\t" "," > tmp && mv tmp tree_stats_table.csv
@@ -285,8 +296,8 @@ else
 fi
 
 #Copy results to home
-cp tree_stats_table.csv $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
-cp *.png $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+cp tree_stats_table.csv $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+cp *.png $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
 #Remove results
 rm *.png
 rm LB*.txt LB*.csv
@@ -318,9 +329,9 @@ if [[ $FastTreeBoot =~ "yes" ]]; then
 	mv LBscores.csv LBscores_bootstrap.csv
 	mv LBscoresPerTaxon.txt LBscoresPerTaxon_bootstrap.txt
 	mv LBscoresSDPerLocus.txt LBscoresSDPerLocus_bootstrap.txt
-	cp LBscores_bootstrap.csv $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
-	cp LBscoresPerTaxon_bootstrap.txt $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
-	cp LBscoresSDPerLocus_bootstrap.txt $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+	cp LBscores_bootstrap.csv $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+	cp LBscoresPerTaxon_bootstrap.txt $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+	cp LBscoresSDPerLocus_bootstrap.txt $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
 	#Combine 'LBscoresSDPerLocus_bootstrap.txt' with 'tree_stats_table.csv'
 	awk '{ print $2 }' LBscoresSDPerLocus_bootstrap.txt > tmp && mv tmp LBscoresSDPerLocus_bootstrap.txt
 	paste tree_stats_table.csv LBscoresSDPerLocus_bootstrap.txt | tr "\t" "," > tmp && mv tmp tree_stats_table.csv
@@ -337,10 +348,10 @@ if [[ $FastTreeBoot =~ "yes" ]]; then
 	fi
 	#Rename results and copy results to home
 	mv tree_stats_table.csv tree_stats_table_bootstrap.csv
-	cp tree_stats_table_bootstrap.csv $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+	cp tree_stats_table_bootstrap.csv $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
 	#Rename all PNG files generated by R (add 'bootstrap')and copy them to home
 	for file in *.png; do mv "$file" "${file/.png/_bootstrap.png}"; done
-	cp *.png $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+	cp *.png $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
 fi
 
 #----------------Combine tree summary table with alignment summary and print comparison plots----------------
@@ -348,7 +359,7 @@ fi
 cp $source/plotting_correlations.R .
 echo -e "Combining alignment and tree properties...\n"
 #Copy alignment summary
-cp $path/$type/71selected${MISSINGPERCENT}/summarySELECTED_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt .
+cp $path/${alnpathselected}${MISSINGPERCENT}/summarySELECTED_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt .
 #***Modify alignment summary***
 #Remove '_Assembly' (now locus names start with a number)
 sed -i.bak 's/Assembly_//g' summarySELECTED*.txt
@@ -405,10 +416,10 @@ if [[ $location == "1" ]]; then
 else
 	R --slave -f plotting_correlations.R >> R.log 2>&1
 fi
-cp genes_corrs.* $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+cp genes_corrs.* $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
 rm genes_corrs.*
 mv combined.txt gene_properties.txt
-cp gene_properties.txt $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+cp gene_properties.txt $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
 
 #Run comparison plots for FastTrees with true bootstrap ('bootstrap')
 if [[ $FastTreeBoot =~ "yes" ]]; then
@@ -424,14 +435,14 @@ if [[ $FastTreeBoot =~ "yes" ]]; then
 	fi
 	mv genes_corrs.png genes_corrs_bootstrap.png
 	mv genes_corrs.pdf genes_corrs_bootstrap.pdf
-	cp genes_corrs_bootstrap.* $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+	cp genes_corrs_bootstrap.* $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
 	rm genes_corrs_bootstrap.*
 	mv combined.txt gene_properties_bootstrap.txt
-	cp gene_properties_bootstrap.txt $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+	cp gene_properties_bootstrap.txt $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
 fi
 
 #Copy R.log to home
-cp R.log $path/$type/72trees${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
+cp R.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree
 
 #Clean scratch/work directory
 if [[ $PBS_O_HOST == *".cz" ]]; then
diff --git a/HybPhyloMaker7_roottrees.sh b/HybPhyloMaker7_roottrees.sh
index d871b99..f032912 100644
--- a/HybPhyloMaker7_roottrees.sh
+++ b/HybPhyloMaker7_roottrees.sh
@@ -19,8 +19,8 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                          Script 07 - Root gene trees                         *
-# *                                   v.1.3.2                                    *
-# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
+# *                                   v.1.4.0                                    *
+# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * tomas.fer@natur.cuni.cz                                                      *
 # ********************************************************************************
 
diff --git a/HybPhyloMaker8a_astral.sh b/HybPhyloMaker8a_astral.sh
index 88a492f..f3d72ae 100644
--- a/HybPhyloMaker8a_astral.sh
+++ b/HybPhyloMaker8a_astral.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 #----------------MetaCentrum----------------
 #PBS -l walltime=2h
-#PBS -l nodes=1:ppn=4
+#PBS -l nodes=1:ppn=4:debian8:minspec=29
 #PBS -j oe
 #PBS -l mem=16gb
 #PBS -l scratch=2gb
@@ -21,8 +21,8 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                       Script 08a - Astral species tree                       *
-# *                                   v.1.3.1                                    *
-# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
+# *                                   v.1.4.0                                    *
+# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * tomas.fer@natur.cuni.cz                                                      *
 # ********************************************************************************
 
@@ -52,6 +52,7 @@ if [[ $PBS_O_HOST == *".cz" ]]; then
 	module add python27-modules-gcc
 	module add python-3.4.1-intel
 	module add newick-utils-1.6
+	module add p4
 elif [[ $HOSTNAME == compute-*-*.local ]]; then
 	echo -e "\nHybPhyloMaker8a is running on Hydra..."
 	#settings for Hydra
@@ -66,6 +67,7 @@ elif [[ $HOSTNAME == compute-*-*.local ]]; then
 	module load java/1.7
 	module load bioinformatics/anaconda3/2.3.0
 	module load bioinformatics/newickutilities/0.0
+	module load bioinformatics/p4/ #???
 else
 	echo -e "\nHybPhyloMaker8a is running locally..."
 	#settings for local run
diff --git a/HybPhyloMaker8b_astrid.sh b/HybPhyloMaker8b_astrid.sh
index b4fa887..dac43bb 100644
--- a/HybPhyloMaker8b_astrid.sh
+++ b/HybPhyloMaker8b_astrid.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 #----------------MetaCentrum----------------
 #PBS -l walltime=2h
-#PBS -l nodes=1:ppn=4
+#PBS -l nodes=1:ppn=4:debian8
 #PBS -j oe
 #PBS -l mem=8gb
 #PBS -N HybPhyloMaker8b_Astrid
@@ -20,8 +20,8 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                       Script 08b - Astrid species tree                       *
-# *                                   v.1.3.2                                    *
-# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
+# *                                   v.1.4.0                                    *
+# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * tomas.fer@natur.cuni.cz                                                      *
 # ********************************************************************************
 
@@ -53,6 +53,7 @@ if [[ $PBS_O_HOST == *".cz" ]]; then
 	module add python27-modules-gcc
 	module add python-3.4.1-intel
 	module add newick-utils-1.6
+	module add p4
 elif [[ $HOSTNAME == *local* ]]; then
 	echo -e "\nHybPhyloMaker8b is running on Hydra..."
 	#settings for Hydra
@@ -66,6 +67,7 @@ elif [[ $HOSTNAME == *local* ]]; then
 	#Add necessary modules
 	module load bioinformatics/anaconda3/2.3.0
 	module load bioinformatics/newickutilities/0.0
+	module load bioinformatics/p4/ #???
 else
 	echo -e "\nHybPhyloMaker8b is running locally..."
 	#settings for local run
diff --git a/HybPhyloMaker8c_mrl.sh b/HybPhyloMaker8c_mrl.sh
index e7f4ff8..acce073 100644
--- a/HybPhyloMaker8c_mrl.sh
+++ b/HybPhyloMaker8c_mrl.sh
@@ -21,8 +21,8 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                        Script 08c - MRL species tree                         *
-# *                                   v.1.3.1                                    *
-# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
+# *                                   v.1.4.0                                    *
+# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * tomas.fer@natur.cuni.cz                                                      *
 # ********************************************************************************
 
diff --git a/HybPhyloMaker8e_concatenatedFastTree.sh b/HybPhyloMaker8e_concatenatedFastTree.sh
index e21b749..74a086c 100644
--- a/HybPhyloMaker8e_concatenatedFastTree.sh
+++ b/HybPhyloMaker8e_concatenatedFastTree.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 #----------------MetaCentrum----------------
 #PBS -l walltime=2d
-#PBS -l nodes=1:ppn=8
+#PBS -l nodes=1:ppn=8:minspec=29
 #PBS -j oe
 #PBS -l mem=24gb
 #PBS -l scratch=8gb
@@ -21,8 +21,8 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                    Script 08e - concatenated species tree                    *
-# *                                   v.1.3.1                                    *
-# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
+# *                                   v.1.4.0                                    *
+# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * tomas.fer@natur.cuni.cz                                                      *
 # ********************************************************************************
 
diff --git a/HybPhyloMaker8f_concatenatedExaML.sh b/HybPhyloMaker8f_concatenatedExaML.sh
index b09891f..e3dcb6f 100644
--- a/HybPhyloMaker8f_concatenatedExaML.sh
+++ b/HybPhyloMaker8f_concatenatedExaML.sh
@@ -1,17 +1,17 @@
 #!/bin/bash
 #PBS -l walltime=2d
-#PBS -l nodes=4:ppn=16:infiniband
+#PBS -l nodes=1:ppn=12:minspec=29
 #PBS -j oe
 #PBS -l mem=4gb
-#PBS -l scratch=32gb:shared
+#PBS -l scratch=32gb
 #PBS -N HybPhyloMaker8f_ExaMLconcatenated_tree
 #PBS -m abe
 
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                     Script 08f - ExaML concatenated tree                     *
-# *                                   v.1.3.2                                    *
-# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
+# *                                   v.1.4.0                                    *
+# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * tomas.fer@natur.cuni.cz                                                      *
 # ********************************************************************************
 
@@ -222,7 +222,7 @@ else
 	module add hdf5-1.8.12-gcc
 	# Run PartitionFinder
 	#python partitionfinder/PartitionFinder.py PartitionFinder --raxml --rcluster-max 1000 --rcluster-percent 10
-	python partitionfinder/PartitionFinder.py PartitionFinder --raxml
+	python partitionfinder/PartitionFinder.py -p $TORQUE_RESC_TOTAL_PROCS PartitionFinder --raxml
 	#Prepare RAxML (ExaML) partition file from PartitionFinder results
 	grep "DNA, Subset" PartitionFinder/analysis/best_scheme.txt > RAxMLpartitions.txt
 	echo -e "\nPartitionFinder finished...\n"
diff --git a/HybPhyloMaker9_update_trees.sh b/HybPhyloMaker9_update_trees.sh
index b8cafc1..c46ee5a 100644
--- a/HybPhyloMaker9_update_trees.sh
+++ b/HybPhyloMaker9_update_trees.sh
@@ -19,8 +19,8 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                           Script 09 - Update trees                           *
-# *                                   v.1.3.2                                    *
-# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
+# *                                   v.1.4.0                                    *
+# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * tomas.fer@natur.cuni.cz                                                      *
 # ********************************************************************************
 
@@ -166,7 +166,7 @@ cp *histogram.png $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/
 #Copy R.log to home
 cp R.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/
 #Prepare list of genes of updated selection
-cat gene_properties_update.txt | sed 1d | cut -f1 | sort | sed 's/Corrected/CorrectedAssembly_/g' | sed "s/_modif${MISSINGPERCENT}.fas//g" > selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt
+cat gene_properties_update.txt | sed 1d | cut -f1 | sort | sed 's/Corrected//g' | sed "s/_modif${MISSINGPERCENT}.fas//g" > selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt
 mkdir -p $path/${alnpathselected}${MISSINGPERCENT}/updatedSelectedGenes
 cp selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt $path/${alnpathselected}${MISSINGPERCENT}/updatedSelectedGenes
 echo -e "\nList of updated selected genes saved to $path/${alnpathselected}${MISSINGPERCENT}/updatedSelectedGenes/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt..."
diff --git a/install_software.sh b/install_software.sh
index a40ce8a..20abce1 100644
--- a/install_software.sh
+++ b/install_software.sh
@@ -5,10 +5,10 @@
 # Without changes works only on 64-bit platforms (x86_64)                                                                #
 # This script MUST be run with root privileges!                                                                          #
 #                                                                                                                        #
-# Tomas Fer, 2016                                                                                                        #
+# Tomas Fer, 2017                                                                                                        #
 # tomas.fer@natur.cuni.cz                                                                                                #
 # https://github.com/tomas-fer/HybPhyloMaker                                                                             #
-# v.1.3.2                                                                                                                #
+# v.1.4.0                                                                                                                #
 ##########################################################################################################################
 
 #Carefully set your distribution
@@ -59,7 +59,7 @@ if ! [ -x "$(command -v python)" ]; then
 	$installer install -y python &> python_install.log
 fi
 
-#Python3
+#Python3 (+ Biopython)
 if ! [ -x "$(command -v python3)" ]; then
 	if [[ $distribution =~ "CentOS" ]]; then
 		echo -e "Installing 'python3'"
@@ -68,9 +68,33 @@ if ! [ -x "$(command -v python3)" ]; then
 	else
 		echo -e "Installing 'python3'"
 		$installer install -y python3 &> python3_install.log #Does not work on CentOS
+		
 	fi
 fi
 
+#Pip
+if ! [ -x "$(command -v pip)" ]; then
+	echo -e "Installing 'pip'"
+	$installer install -y python-pip &> pip_install.log
+fi
+
+#Pip3 (also required for 'kindel' installation, see below)
+if ! [ -x "$(command -v pip3)" ]; then
+	if [[ $distribution =~ "CentOS" ]]; then
+		echo -e "Installing 'pip3'"
+		$installer install -y python34-devel &>> python3_install.log #Only for CentOS
+		$installer install -y python34-pip &> pip3_install.log #Only for CentOS
+	else
+		echo -e "Installing 'pip3'"
+		$installer install -y python3-dev &>> python3_install.log #Does not work on CentOS
+		$installer install -y python3-pip &> pip3_install.log #Does not work on CentOS
+	fi
+fi
+
+#Biopython
+echo -e "Installing 'biopython'"
+pip3 install biopython &> biopython_install.log
+
 #Java
 if [[ $distribution =~ "Debian" ]]; then
 	echo -e "Installing 'java'"
@@ -104,15 +128,9 @@ elif [[ $distribution =~ "Fedora" ]] || [[ $distribution =~ "CentOS" ]]; then
 fi
 
 #R
-#Comment for Ubuntu: you should install the newest version of R by adding CRAN mirror to /etc/apt/sources.list
-#(see, e.g., https://cran.r-project.org/bin/linux/ubuntu/README.html)
-# codename=$(lsb_release -c -s)
-# echo "deb http://cran.cnr.berkeley.edu/bin/linux/ubuntu $codename/" | sudo tee -a /etc/apt/sources.list > /dev/null
-# apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
-# add-apt-repository ppa:marutter/rdev
-# apt-get update
-# apt-get upgrade
-# apt-get install -y r-base r-base-dev
+#Comment for Ubuntu/Debian: you should install the newest version of R by adding CRAN mirror to /etc/apt/sources.list
+#Look at the end of this script for an advice how to do that...
+#Newer version (i.e., at least v3.2) should be installed before running this script!
 if [[ $distribution =~ "Debian" ]]; then
 	echo -e "Installing 'R'"
 	$installer install -y r-base-dev &> R_install.log #Debian/Ubuntu
@@ -221,6 +239,20 @@ if ! [ -x "$(command -v FastTree)" ]; then
 	cd ..
 fi
 
+#EMBOSS
+if ! [ -x "$(command -v transeq)" ]; then
+	echo -e "Installing 'EMBOSS'"
+	wget ftp://emboss.open-bio.org/pub/EMBOSS/emboss-latest.tar.gz &> ../EMBOSS_install.log
+	tar xfz emboss-latest.tar.gz 1>/dev/null
+	rm emboss-latest.tar.gz
+	cd EMBOSS*
+	./configure &>> ../EMBOSS_install.log
+	make &>> ../EMBOSS_install.log
+	ldconfig
+	make install &>> ../EMBOSS_install.log
+	cd ..
+fi
+
 #RAxML
 git clone https://github.com/stamatak/standard-RAxML &> raxml_install.log
 cd standard-RAxML
@@ -354,6 +386,12 @@ if ! [ -x "$(command -v ococo)" ]; then
 	cd ..
 fi
 
+#kindel (necessary for majority rule consensus building from mapped reads in BAM file)
+#see https://pypi.python.org/pypi/kindel
+if ! [ -x "$(command -v kindel)" ]; then
+	pip3 install kindel &>> kindel_install.log
+fi
+
 #p4 (only necessary for combining bootstrap support in Astral and Astrid trees)
 #see http://p4.nhm.ac.uk/installation.html
 #For compilation on Fedora/CentOS/OpenSUSE you need to specify where 'gsl' is installed (in setup.py) - modification of 'setup.py' is included below
@@ -381,14 +419,16 @@ if ! [ -x "$(command -v p4)" ]; then
 	if [[ $distribution =~ "Fedora" ]] || [[ $distribution =~ "CentOS" ]]; then
 		$installer install redhat-rpm-config &> rpm-config_install.log
 	fi
+	#install python module 'future'
+	pip install future &> python-future_install.log
 	
 	git clone https://github.com/pgfoster/p4-phylogenetics &> p4_install.log
 	cd p4-phylogenetics
 	#Modify setup.py to be able to find gsl
 	if [[ $distribution =~ "OpenSUSE" ]] || [[ $distribution =~ "CentOS" ]] || [[ $distribution =~ "Fedora" ]]; then
 		replace="my_include_dirs = [\'\/usr\/include\/\']"
-		sed -i.bak "45s/.*/$replace/" setup.py
-		sed -i.bak2 "46s/# //" setup.py
+		sed -i.bak "46s/.*/$replace/" setup.py
+		sed -i.bak2 "47s/# //" setup.py
 	fi
 	python setup.py build &>> ../p4_install.log
 	python setup.py install &>> ../p4_install.log
@@ -402,7 +442,7 @@ cd ..
 #Check if everything is installed correctly
 echo -e "\n**************************************************************"
 echo -e "Software installed...checking for binaries in PATH"
-for i in parallel bowtie2 ococo samtools bam2fastq java fastuniq perl blat mafft python python3 trimal mstatx FastTree nw_reroot nw_topology raxmlHPC raxmlHPC-PTHREADS R p4; do
+for i in parallel bowtie2 ococo kindel samtools transeq bam2fastq java fastuniq perl blat mafft python python3 trimal mstatx FastTree nw_reroot nw_topology raxmlHPC raxmlHPC-PTHREADS R p4; do
 	command -v $i >/dev/null 2>&1 || { echo -n $i; echo >&2 "...not found"; }
 done
 
@@ -433,7 +473,7 @@ echo -e "\nInstalation script finished.\n"
 
 # Successfully tested on
 # - Ubuntu 14.04 LTS #Newer R version necessary, see below!!!
-# - Debian 8.6
+# - Debian 8.6 #Newer R version necessary, see below!!!
 # - OpenSUSE 42
 # - CentOS 7.2
 # - Fedora 24
@@ -465,14 +505,13 @@ echo -e "\nInstalation script finished.\n"
 #NewickUtilities will not work!
 
 #**********************************************************************************
-#Debian 7
+#Debian 7, 8
 #too old R version (see https://cran.r-project.org/bin/linux/debian/ how to update)
 # codename=$(lsb_release -c -s)
 # echo "deb http://cran.cnr.berkeley.edu/bin/linux/debian ${codename}-cran3/" | sudo tee -a /etc/apt/sources.list > /dev/null
 # apt-key adv --keyserver keys.gnupg.net --recv-key 6212B7B7931C4BB16280BA1306F90DE5381BA480
-# apt-get install -y r-base r-base-dev
 # apt-get update
 # apt-get upgrade
 #
-#and too old glibc. GLIBC_2.14 is required - and it is not easy to upgrade, better to upgrade to Debian 8
+#only Debian 7 - too old glibc. GLIBC_2.14 is required - and it is not easy to upgrade, better to upgrade to Debian 8
 #NewickUtilities will not work!
diff --git a/settings.cfg b/settings.cfg
index 0f0fae0..704c337 100644
--- a/settings.cfg
+++ b/settings.cfg
@@ -1,8 +1,8 @@
 #****************************************
 #* Configuration file for HybPhyloMaker *
-#* Tomas Fer, 2016                      *
+#* Tomas Fer, 2017                      *
 #* tomas.fer@natur.cuni.cz              *
-#* v.1.3.2                              *
+#* v.1.4.0                              *
 #****************************************
 
 #--------------------------------------------------------------------------------------------------------------------
@@ -26,8 +26,9 @@ tree=FastTree
 #Bootstrap FastTree (yes/no). no=normal FastTree with local branch support, very fast; yes=FastTree is applied to each of 100 bootstrap replicates, slow
 FastTreeBoot=no
 
-#Use 'by exon partitioning' when building gene trees with RAxML (yes/no)
-genetreepart=yes
+#Use 'no', 'by exon' or 'by codon and exon' partitioning when building gene trees with RAxML (no, exon, codon)
+#Codon is only for the data with corrected reading frame!
+genetreepart=exon
 
 #Outgroup (as it appears in RAxML files)
 OUTGROUP="Siphonochilus-aethiopicus_S130"
@@ -56,6 +57,12 @@ cp=no
 #Working with updated list of genes (yes/no)
 update=no
 
+#Working with corrected reading frame for exons/genes (yes/no) - not yet fully implemented
+corrected=yes
+
+#Maximum number of stop codons allowed per alignment (i.e., considered as errors)
+maxstop=5
+
 #--------------------------------------------------------------------------------------------------------------------
 # **** REFERENCE FILES ****
 #--------------------------------------------------------------------------------------------------------------------
@@ -128,10 +135,13 @@ raxmlperjob=20
 #whether mapping using bowtie2 should be done (yes/no)
 mapping=yes
 
+#consensus calling software (kindel/ococo)
+conscall=kindel
+
 #minimum site coverage for SNP calling (N will be in consensus for sites with lower coverage)
 mincov=2
 
-#majority threshold for consensus calling (0-1)
+#majority threshold for consensus calling (0-1) - not working in OCOCO!
 majthres=0.51
 
 #--------------------------------------------------------------------------------------------------------------------