diff --git a/CHANGES.txt b/CHANGES.txt index 8722595..bf0ef6c 100644 --- a/CHANGES.txt +++ b/CHANGES.txt @@ -406,3 +406,5 @@ 22032023: annotate_cluster.pl -u produces unaligned complete sequences, flipped if required to facilitate multiple alignments 28032023: added more dependencies required for compiling R packages in install_R_deps.R 05052023: check that download_genomes_ncbi.pl still works with sample_genome.list +15052023: updated BLAST to faster, smaller ncbi-blast-2.14.0+ binaries +15052022: update install.pl and updated bin.tgz (v3.6) diff --git a/install.pl b/install.pl index b615fe1..593d042 100755 --- a/install.pl +++ b/install.pl @@ -2,7 +2,7 @@ # Script that checks/compiles software required by get_homologues[-est] and # checks dependencies for first-time users. -# last checked Apr2022 +# last checked May2023 use strict; use warnings; @@ -20,8 +20,8 @@ my $DOWNLOADEXE = 'wget'; # add path if required, curl in MacOS my $BINTGZFILE = 'bin.tgz'; my $BINOSXTGZFILE = 'binosx.tgz'; -my $BINURL = "https://github.com/eead-csic-compbio/get_homologues/releases/download/v3.5/$BINTGZFILE"; -my $BINOSXURL = "https://github.com/eead-csic-compbio/get_homologues/releases/download/v3.5/$BINOSXTGZFILE"; +my $BINURL = "https://github.com/eead-csic-compbio/get_homologues/releases/download/v3.6/$BINTGZFILE"; +my $BINOSXURL = "https://github.com/eead-csic-compbio/get_homologues/releases/download/v3.6/$BINOSXTGZFILE"; my $PFAMSERVERURL = 'ftp.ebi.ac.uk'; my $PFAMFOLDER = 'pub/databases/Pfam/current_release/'; @@ -40,7 +40,7 @@ 'GD'=>['libgd-gd2-perl','perl-GD','perl-GD','gd'] ); -my $nonCOGS = 'diamond-0.8.25 hmmer-3.1b2 mcl-14-137 ncbi-blast-2.8.1+ phylip-3.695'; +my $nonCOGS = 'diamond-0.8.25 hmmer-3.1b2 mcl-14-137 ncbi-blast-2.14.0+ phylip-3.695'; my ($SOguess,$output,$command,$cwd) = ('','','',getcwd()); my ($downloadOK,$force_unsupervised,$noDBs) = (0,0,0); @@ -244,7 +244,7 @@ print "## Checking blast (lib/phyTools: \$ENV{'EXE_BLASTP'})\n"; if($downloadOK){ - $ENV{'EXE_BLASTP'} = $ENV{'MARFIL'}."/bin/ncbi-blast-2.8.1+/bin/blastp" + $ENV{'EXE_BLASTP'} = $ENV{'MARFIL'}."/bin/ncbi-blast-2.14.0+/bin/blastp" } $output = `$ENV{'EXE_BLASTP'} 2>&1`; diff --git a/lib/phyTools.pm b/lib/phyTools.pm index a937ae7..a95ceb2 100755 --- a/lib/phyTools.pm +++ b/lib/phyTools.pm @@ -1,5 +1,5 @@ # Bruno Contreras-Moreira, Pablo Vinuesa -# 2005-22 CCG/UNAM, Mexico, EEAD/CSIC, Zaragoza, Spain +# 2005-23 CCG/UNAM, Mexico, EEAD/CSIC, Zaragoza, Spain # This is a collection of subroutines used in our projects, # including primers4clades and get_homologues @@ -87,7 +87,7 @@ sub set_phyTools_env # BLAST if( ! defined($ENV{'BLAST_PATH'}) ){ - $ENV{'BLAST_PATH'} = $ENV{'MARFIL'}.'bin/ncbi-blast-2.8.1+/bin/'; + $ENV{'BLAST_PATH'} = $ENV{'MARFIL'}.'bin/ncbi-blast-2.14.0+/bin/'; if(!-e $ENV{'BLAST_PATH'}){ $ENV{'BLAST_PATH'} = ''; # should work if in PATH } diff --git a/manual_get_homologues-est.pdf b/manual_get_homologues-est.pdf index 4e18cc5..de43941 100644 Binary files a/manual_get_homologues-est.pdf and b/manual_get_homologues-est.pdf differ diff --git a/manual_get_homologues.pdf b/manual_get_homologues.pdf index 66a3e12..bfc4e8b 100644 Binary files a/manual_get_homologues.pdf and b/manual_get_homologues.pdf differ diff --git a/sample_intersection/intersection_t0.cluster_list b/sample_intersection/intersection_t0.cluster_list index d058bea..4f17c67 100755 --- a/sample_intersection/intersection_t0.cluster_list +++ b/sample_intersection/intersection_t0.cluster_list @@ -3,184 +3,184 @@ # -o sample_intersection # -I # -r 0 -225_delta-FipA.faa -294_hypothetical_protein.faa -233_YdaA.faa -9_mphA.faa -280_transposase.faa -631_traI.faa +348_group_II_intron-enco...faa +618_traM.faa +73_mph2.faa +624_traN.faa +632_traJ.faa +173_arsR.faa +362_group_II_intron-enco...faa 643_ccgEIII.faa -636_stbC.faa -243_TnpM.faa -7_transposase_A.faa -229_QnrS1.faa -242_TnpA.faa -635_stbB.faa -626_traO.faa +614_hypothetical_protein.faa +302_conserved_hypothetic...faa +338_InsB.faa +629_nuc.faa 637_hypothetical_protein.faa -647_mucB.faa -166_unknown.faa -168_unknown.faa -381_hypothetical_protein.faa -634_stbA.faa -438_unknown.faa -198_TnpA.faa -240_putative_invertase-r...faa -289_beta-lactamase.faa -624_traN.faa -245_dfrA14.faa -250_putative_mobilizatio...faa -604_dcm.faa -743_putative_IS91_ORF2.faa 603_ecoRII.faa -282_hypothetical_protein.faa -176_arsB.faa -341_hypothetical_protein.faa -238_TnpA.faa -471_putative_relaxase-he...faa -364_conserved_hypothetic...faa -379_hypothetical_protein.faa -286_streptomycin_phospho...faa -11_blaCTX-M-1.faa -645_ardB.faa -376_hypothetical_protein.faa -641_ccgC.faa -255_hypothetical_protein.faa -629_nuc.faa -297_hypothetical_protein.faa -65_sul1.faa -618_traM.faa -201_VIM-1.faa -172_unknown.faa -69_hypothetical_protein.faa -367_ISEc8_transposase.faa -234_hypothetical_protein.faa -173_arsR.faa -301_putative_transposase.faa -241_PilT.faa -352_resolvase.faa -639_ccgAI.faa +74_hypothetical_protein.faa +605_hypothetical_protein.faa +621_traC.faa +232_hypothetical_protein.faa +245_dfrA14.faa +438_unknown.faa +608_tetB.faa 444_FosA.faa -299_site-specific_recomb...faa -609_tetR.faa -35_tnpA.faa +641_ccgC.faa 363_putative_transposase...faa -235_hypothetical_protein.faa -416_TraL.faa -417_hypothetical_protein.faa -648_mpr.faa -177_arsC.faa -557_insF.faa -382_conserved_hypothetic...faa -642_ccgD.faa -232_hypothetical_protein.faa -72_mph1.faa -366_excinuclease_ABC-_A_...faa -174_arsD.faa -350_transposase.faa -620_traB.faa -175_arsA.faa -302_conserved_hypothetic...faa -638_ccgAII.faa -383_hypothetical_protein.faa -390_hypothetical_protein.faa 296_hypothetical_protein.faa -420_hypothetical_protein.faa -616_traL.faa -528_MAK2.40.faa -348_group_II_intron-enco...faa -71_mel.faa -318_TraB.faa -625_traE.faa -295_hypothetical_protein.faa -649_ardK.faa -321_arsenical_pump-drivi...faa -159_intI1.faa -10_mrx.faa -640_ardA.faa -619_traA.faa +622_eex.faa +626_traO.faa 547_insA.faa -368_hypothetical_protein.faa -605_hypothetical_protein.faa -391_hypothetical_protein.faa -268_hypothetical_protein.faa -246_hypothetical_protein.faa -613_kikA.faa -353_S-formylglutathione_...faa -495_MAK2.05.faa -163_unknown.faa 61_linF.faa -621_traC.faa -448_hypothetical_protein.faa -338_InsB.faa -548_insB.faa -602_resP.faa -365_NADH_dehydrogenase-_...faa +471_putative_relaxase-he...faa +175_arsA.faa +607_tetC.faa +298_conserved_hypothetic...faa +364_conserved_hypothetic...faa +70_tnpD.faa 615_korB.faa -744_tnp.faa +200_AacA4.faa +390_hypothetical_protein.faa +602_resP.faa 60_ant3-9.faa -630_fipA.faa -34_methyl-accepting_che...faa +617_korA.faa 445_tnpA.faa -236_putative_DeoR-type_t...faa -70_tnpD.faa -384_hypothetical_protein.faa -298_conserved_hypothetic...faa -308_conserved_hypothetic...faa -68_armA.faa -402_conserved_hypothetic...faa -171_unknown.faa -606_type_IV_restriction_...faa +646_mucA.faa 396_TraK.faa -628_traG.faa -13_hypothetical_protein.faa 226_TnpA.faa -73_mph2.faa -632_traJ.faa -617_korA.faa +606_type_IV_restriction_...faa +299_site-specific_recomb...faa +268_hypothetical_protein.faa +174_arsD.faa +243_TnpM.faa 253_transposition_modula...faa -87_traA.faa -288_resolvase.faa -380_hypothetical_protein.faa -304_transposase-_IS4_fam...faa -623_traD.faa -501_yahA.faa -627_traF.faa -408_hypothetical_protein.faa -401_protein_of_unknown_f...faa -307_hypothetical_protein.faa -601_repA.faa -200_AacA4.faa +367_ISEc8_transposase.faa +293_hypothetical_protein.faa 644_ardR.faa -355_S--hydroxymethyl-glu...faa -614_hypothetical_protein.faa -281_phage_integrase_fami...faa -435_ampR.faa -633_traK.faa +13_hypothetical_protein.faa +402_conserved_hypothetic...faa +381_hypothetical_protein.faa +230_hypothetical_protein.faa +365_NADH_dehydrogenase-_...faa +250_putative_mobilizatio...faa 413_TraA.faa -607_tetC.faa -497_ble.faa +69_hypothetical_protein.faa +616_traL.faa +501_yahA.faa +648_mpr.faa +72_mph1.faa +630_fipA.faa 36_beta-lactamase_CTX-M...faa -74_hypothetical_protein.faa -523_pecM.faa +321_arsenical_pump-drivi...faa +66_hypothetical_protein.faa +71_mel.faa +168_unknown.faa +282_hypothetical_protein.faa +264_hypothetical_protein.faa +645_ardB.faa +304_transposase-_IS4_fam...faa +642_ccgD.faa +163_unknown.faa +631_traI.faa +380_hypothetical_protein.faa +354_glyoxalase-bleomycin...faa +171_unknown.faa +341_hypothetical_protein.faa +640_ardA.faa +236_putative_DeoR-type_t...faa +240_putative_invertase-r...faa +297_hypothetical_protein.faa +351_putative_transposase...faa +242_TnpA.faa +235_hypothetical_protein.faa +619_traA.faa +9_mphA.faa +382_conserved_hypothetic...faa +280_transposase.faa +636_stbC.faa +497_ble.faa +160_oxa2.faa 231_hypothetical_protein.faa -230_hypothetical_protein.faa -8_tnpA.faa +11_blaCTX-M-1.faa +649_ardK.faa +379_hypothetical_protein.faa +611_strB.faa +528_MAK2.40.faa +201_VIM-1.faa +238_TnpA.faa +172_unknown.faa +10_mrx.faa 228_truncated_TnpA.faa -351_putative_transposase...faa -400_DNA_polymerase-_beta...faa +417_hypothetical_protein.faa +166_unknown.faa +523_pecM.faa +34_methyl-accepting_che...faa +634_stbA.faa +35_tnpA.faa +233_YdaA.faa +307_hypothetical_protein.faa 64_qacEdelta1.faa -66_hypothetical_protein.faa -160_oxa2.faa +294_hypothetical_protein.faa +241_PilT.faa +627_traF.faa +159_intI1.faa +352_resolvase.faa +376_hypothetical_protein.faa +68_armA.faa +353_S-formylglutathione_...faa +628_traG.faa +198_TnpA.faa +246_hypothetical_protein.faa +255_hypothetical_protein.faa +368_hypothetical_protein.faa +638_ccgAII.faa +623_traD.faa +548_insB.faa +408_hypothetical_protein.faa +635_stbB.faa +318_TraB.faa +448_hypothetical_protein.faa +384_hypothetical_protein.faa +495_MAK2.05.faa +8_tnpA.faa +633_traK.faa +613_kikA.faa +7_transposase_A.faa 349_transposase_InsF.faa -327_TraB.faa -354_glyoxalase-bleomycin...faa -608_tetB.faa -264_hypothetical_protein.faa -646_mucA.faa +350_transposase.faa +647_mucB.faa +177_arsC.faa +401_protein_of_unknown_f...faa +295_hypothetical_protein.faa +383_hypothetical_protein.faa +366_excinuclease_ABC-_A_...faa +308_conserved_hypothetic...faa +355_S--hydroxymethyl-glu...faa +391_hypothetical_protein.faa +604_dcm.faa +176_arsB.faa +743_putative_IS91_ORF2.faa +416_TraL.faa +229_QnrS1.faa +435_ampR.faa 498_sph.faa -611_strB.faa -293_hypothetical_protein.faa -362_group_II_intron-enco...faa -622_eex.faa +620_traB.faa +625_traE.faa +744_tnp.faa +601_repA.faa +420_hypothetical_protein.faa +301_putative_transposase.faa +557_insF.faa +639_ccgAI.faa +286_streptomycin_phospho...faa +87_traA.faa +327_TraB.faa +400_DNA_polymerase-_beta...faa +289_beta-lactamase.faa +281_phage_integrase_fami...faa +65_sul1.faa +234_hypothetical_protein.faa +225_delta-FipA.faa +288_resolvase.faa +609_tetR.faa # intersection size = 180 clusters diff --git a/sample_intersection/pangenome_matrix_t0__shell.pdf b/sample_intersection/pangenome_matrix_t0__shell.pdf index c1c8efa..bae0b85 100644 Binary files a/sample_intersection/pangenome_matrix_t0__shell.pdf and b/sample_intersection/pangenome_matrix_t0__shell.pdf differ diff --git a/sample_intersection/pangenome_matrix_t0__shell_circle.pdf b/sample_intersection/pangenome_matrix_t0__shell_circle.pdf index 601fcbe..2a9291f 100755 Binary files a/sample_intersection/pangenome_matrix_t0__shell_circle.pdf and b/sample_intersection/pangenome_matrix_t0__shell_circle.pdf differ diff --git a/sample_intersection/unique_UnculturedbacteriumplasmidpRSB203_f0_0taxa_algCOG_e0_.venn_t0.txt b/sample_intersection/unique_UnculturedbacteriumplasmidpRSB203_f0_0taxa_algCOG_e0_.venn_t0.txt index 50dc651..8726e10 100644 --- a/sample_intersection/unique_UnculturedbacteriumplasmidpRSB203_f0_0taxa_algCOG_e0_.venn_t0.txt +++ b/sample_intersection/unique_UnculturedbacteriumplasmidpRSB203_f0_0taxa_algCOG_e0_.venn_t0.txt @@ -1,16 +1,16 @@ -305_transposase.faa -178_recombinase.faa 300_transposase.faa -279_transposase.faa -612_hypothetical_protein.faa -527_tnpR.faa -496_aph.faa 247_TnpA.faa +612_hypothetical_protein.faa 610_strA.faa +214_hypothetical_protein.faa +33_tnpA.faa 57_transposase.faa +496_aph.faa +527_tnpR.faa 335_conserved_hypothetic...faa -33_tnpA.faa -204_hypothetical_protein.faa 377_hypothetical_protein.faa +279_transposase.faa +204_hypothetical_protein.faa 526_tnpA.faa -214_hypothetical_protein.faa +305_transposase.faa +178_recombinase.faa diff --git a/sample_intersection/unique_UnculturedbacteriumplasmidpRSB203_f0_0taxa_algOMCL_e0_.venn_t0.txt b/sample_intersection/unique_UnculturedbacteriumplasmidpRSB203_f0_0taxa_algOMCL_e0_.venn_t0.txt index 6fa433b..9aa6d84 100644 --- a/sample_intersection/unique_UnculturedbacteriumplasmidpRSB203_f0_0taxa_algOMCL_e0_.venn_t0.txt +++ b/sample_intersection/unique_UnculturedbacteriumplasmidpRSB203_f0_0taxa_algOMCL_e0_.venn_t0.txt @@ -1,13 +1,13 @@ -279_transposase.faa -204_hypothetical_protein.faa -612_hypothetical_protein.faa -178_recombinase.faa -319_transposase.faa 305_transposase.faa -450_tnpA.faa -610_strA.faa +178_recombinase.faa +204_hypothetical_protein.faa 385_hypothetical_protein.faa 300_transposase.faa -214_hypothetical_protein.faa +612_hypothetical_protein.faa 205_hypothetical_protein.faa +279_transposase.faa +610_strA.faa 33_tnpA.faa +450_tnpA.faa +319_transposase.faa +214_hypothetical_protein.faa diff --git a/sample_intersection/venn_t0.pdf b/sample_intersection/venn_t0.pdf index 078648d..4674e40 100644 Binary files a/sample_intersection/venn_t0.pdf and b/sample_intersection/venn_t0.pdf differ diff --git a/sample_plasmids_gbk_homologues/E_coli_ST131_plasmid_pKC394.gb.fasta.pin b/sample_plasmids_gbk_homologues/E_coli_ST131_plasmid_pKC394.gb.fasta.pin index 9b42e84..3551da9 100755 Binary files a/sample_plasmids_gbk_homologues/E_coli_ST131_plasmid_pKC394.gb.fasta.pin and b/sample_plasmids_gbk_homologues/E_coli_ST131_plasmid_pKC394.gb.fasta.pin differ diff --git a/sample_plasmids_gbk_homologues/E_coli_plasmid_pMUR050.gb.fasta.pin b/sample_plasmids_gbk_homologues/E_coli_plasmid_pMUR050.gb.fasta.pin index ba36e3e..b4d1330 100755 Binary files a/sample_plasmids_gbk_homologues/E_coli_plasmid_pMUR050.gb.fasta.pin and b/sample_plasmids_gbk_homologues/E_coli_plasmid_pMUR050.gb.fasta.pin differ diff --git a/sample_plasmids_gbk_homologues/IncN_plasmid_R46.gb.fasta.pin b/sample_plasmids_gbk_homologues/IncN_plasmid_R46.gb.fasta.pin index 75f0941..6eb49fa 100755 Binary files a/sample_plasmids_gbk_homologues/IncN_plasmid_R46.gb.fasta.pin and b/sample_plasmids_gbk_homologues/IncN_plasmid_R46.gb.fasta.pin differ diff --git a/sample_plasmids_gbk_homologues/K_oxytoca_plasmid_pKOX105.gb.fasta.pin b/sample_plasmids_gbk_homologues/K_oxytoca_plasmid_pKOX105.gb.fasta.pin index 00e7f2c..a169bc9 100755 Binary files a/sample_plasmids_gbk_homologues/K_oxytoca_plasmid_pKOX105.gb.fasta.pin and b/sample_plasmids_gbk_homologues/K_oxytoca_plasmid_pKOX105.gb.fasta.pin differ diff --git a/sample_plasmids_gbk_homologues/K_pneumoniae_12_plasmid_12.gb.fasta.pin b/sample_plasmids_gbk_homologues/K_pneumoniae_12_plasmid_12.gb.fasta.pin index ec4d79b..b05e8f6 100755 Binary files a/sample_plasmids_gbk_homologues/K_pneumoniae_12_plasmid_12.gb.fasta.pin and b/sample_plasmids_gbk_homologues/K_pneumoniae_12_plasmid_12.gb.fasta.pin differ diff --git a/sample_plasmids_gbk_homologues/K_pneumoniae_9_plasmid_9.gb.fasta.pin b/sample_plasmids_gbk_homologues/K_pneumoniae_9_plasmid_9.gb.fasta.pin index 68a7677..867005d 100755 Binary files a/sample_plasmids_gbk_homologues/K_pneumoniae_9_plasmid_9.gb.fasta.pin and b/sample_plasmids_gbk_homologues/K_pneumoniae_9_plasmid_9.gb.fasta.pin differ diff --git a/sample_plasmids_gbk_homologues/K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.pin b/sample_plasmids_gbk_homologues/K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.pin index 832f492..4d6231d 100755 Binary files a/sample_plasmids_gbk_homologues/K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.pin and b/sample_plasmids_gbk_homologues/K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.pin differ diff --git a/sample_plasmids_gbk_homologues/S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.pin b/sample_plasmids_gbk_homologues/S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.pin index 76a691c..17e2eb7 100755 Binary files a/sample_plasmids_gbk_homologues/S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.pin and b/sample_plasmids_gbk_homologues/S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.pin differ diff --git a/sample_plasmids_gbk_homologues/Uncultured_bacterium_plasmid_pRSB201.gb.fasta.pin b/sample_plasmids_gbk_homologues/Uncultured_bacterium_plasmid_pRSB201.gb.fasta.pin index b9b7a99..d0feebc 100755 Binary files a/sample_plasmids_gbk_homologues/Uncultured_bacterium_plasmid_pRSB201.gb.fasta.pin and b/sample_plasmids_gbk_homologues/Uncultured_bacterium_plasmid_pRSB201.gb.fasta.pin differ diff --git a/sample_plasmids_gbk_homologues/Uncultured_bacterium_plasmid_pRSB203.gb.fasta.pin b/sample_plasmids_gbk_homologues/Uncultured_bacterium_plasmid_pRSB203.gb.fasta.pin index fc4a8dc..710321a 100755 Binary files a/sample_plasmids_gbk_homologues/Uncultured_bacterium_plasmid_pRSB203.gb.fasta.pin and b/sample_plasmids_gbk_homologues/Uncultured_bacterium_plasmid_pRSB203.gb.fasta.pin differ diff --git a/sample_plasmids_gbk_homologues/Uncultured_bacterium_plasmid_pRSB205.gb.fasta.pin b/sample_plasmids_gbk_homologues/Uncultured_bacterium_plasmid_pRSB205.gb.fasta.pin index 08954cd..75d701f 100755 Binary files a/sample_plasmids_gbk_homologues/Uncultured_bacterium_plasmid_pRSB205.gb.fasta.pin and b/sample_plasmids_gbk_homologues/Uncultured_bacterium_plasmid_pRSB205.gb.fasta.pin differ diff --git a/sample_plasmids_gbk_homologues/Uncultured_bacterium_plasmid_pRSB206.gb.fasta.pin b/sample_plasmids_gbk_homologues/Uncultured_bacterium_plasmid_pRSB206.gb.fasta.pin index e532e25..c207797 100755 Binary 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differ diff --git a/sample_plasmids_gbk_homologues/_E_coli_plasmid_pMUR050.gb.fasta_IncN_plasmid_R46.gb.fasta.blast.gz b/sample_plasmids_gbk_homologues/_E_coli_plasmid_pMUR050.gb.fasta_IncN_plasmid_R46.gb.fasta.blast.gz index 544ebc9..2da1986 100755 Binary files a/sample_plasmids_gbk_homologues/_E_coli_plasmid_pMUR050.gb.fasta_IncN_plasmid_R46.gb.fasta.blast.gz and b/sample_plasmids_gbk_homologues/_E_coli_plasmid_pMUR050.gb.fasta_IncN_plasmid_R46.gb.fasta.blast.gz differ diff --git a/sample_plasmids_gbk_homologues/_E_coli_plasmid_pMUR050.gb.fasta_K_oxytoca_plasmid_pKOX105.gb.fasta.blast.gz b/sample_plasmids_gbk_homologues/_E_coli_plasmid_pMUR050.gb.fasta_K_oxytoca_plasmid_pKOX105.gb.fasta.blast.gz index 6f2a40a..21bc368 100755 Binary files a/sample_plasmids_gbk_homologues/_E_coli_plasmid_pMUR050.gb.fasta_K_oxytoca_plasmid_pKOX105.gb.fasta.blast.gz and b/sample_plasmids_gbk_homologues/_E_coli_plasmid_pMUR050.gb.fasta_K_oxytoca_plasmid_pKOX105.gb.fasta.blast.gz differ diff --git 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and b/sample_plasmids_gbk_homologues/_E_coli_plasmid_pMUR050.gb.fasta_S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.blast.gz differ diff --git a/sample_plasmids_gbk_homologues/_E_coli_plasmid_pMUR050.gb.fasta_Uncultured_bacterium_plasmid_pRSB201.gb.fasta.blast.gz b/sample_plasmids_gbk_homologues/_E_coli_plasmid_pMUR050.gb.fasta_Uncultured_bacterium_plasmid_pRSB201.gb.fasta.blast.gz index 91f6ce5..2f06a4b 100755 Binary files a/sample_plasmids_gbk_homologues/_E_coli_plasmid_pMUR050.gb.fasta_Uncultured_bacterium_plasmid_pRSB201.gb.fasta.blast.gz and b/sample_plasmids_gbk_homologues/_E_coli_plasmid_pMUR050.gb.fasta_Uncultured_bacterium_plasmid_pRSB201.gb.fasta.blast.gz differ diff --git a/sample_plasmids_gbk_homologues/_E_coli_plasmid_pMUR050.gb.fasta_Uncultured_bacterium_plasmid_pRSB203.gb.fasta.blast.gz b/sample_plasmids_gbk_homologues/_E_coli_plasmid_pMUR050.gb.fasta_Uncultured_bacterium_plasmid_pRSB203.gb.fasta.blast.gz index 49d810b..a7a0929 100755 Binary files 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--git a/sample_plasmids_gbk_homologues/_Uncultured_bacterium_plasmid_pRSB206.gb.fasta_K_pneumoniae_9_plasmid_9.gb.fasta.blast.gz b/sample_plasmids_gbk_homologues/_Uncultured_bacterium_plasmid_pRSB206.gb.fasta_K_pneumoniae_9_plasmid_9.gb.fasta.blast.gz index 1e114a7..4580ec3 100755 Binary files a/sample_plasmids_gbk_homologues/_Uncultured_bacterium_plasmid_pRSB206.gb.fasta_K_pneumoniae_9_plasmid_9.gb.fasta.blast.gz and b/sample_plasmids_gbk_homologues/_Uncultured_bacterium_plasmid_pRSB206.gb.fasta_K_pneumoniae_9_plasmid_9.gb.fasta.blast.gz differ diff --git a/sample_plasmids_gbk_homologues/_Uncultured_bacterium_plasmid_pRSB206.gb.fasta_K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.blast.gz b/sample_plasmids_gbk_homologues/_Uncultured_bacterium_plasmid_pRSB206.gb.fasta_K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.blast.gz index d350213..bb868c7 100755 Binary files a/sample_plasmids_gbk_homologues/_Uncultured_bacterium_plasmid_pRSB206.gb.fasta_K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.blast.gz and 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