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| Original file line number | Diff line number | Diff line change |
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| 15112013: added option core_both to plot_pancore_matrix.pl | ||
| 03022014: corrected versions of get_homologues.pl and parse_pangenome_matrix.pl to match features in manual | ||
| 07032014: manual updated, user's utils added to download area | ||
| 11032014: added use lib/bioperl to compare_clusters.pl and plot_pancore_matrix.pl | ||
| 11032014: edited plot_pancore_matrix.pl (copes with \r in .tab) | ||
| 11032014: added -s to check_BDBHs.pl | ||
| 11032014: updated get_homologues.pl with marfil_homology::add_unmatched_singletons | ||
| 11032014: manual updated | ||
| 18062014: manual updated, added check when reading taxa in -I include file | ||
| 18062014: put new lines to separate alternatives trees in .ph file produced by compare_clusters.pl -T | ||
| 29072014: fixed parsing of GenBank files with CONTIG features just before ORIGIN | ||
| 29072014: fixed parsing of spliced DNA sequence features in GenBank files | ||
| 28082014: sped up id lookup in check_BDBHs.pl | ||
| 01092014: manual updated | ||
| 30092014: install.pl fixed so that progress of Pfam download is correctly printed | ||
| 24102014: manual updated (-f explanation. FAQS) | ||
| 12112014: fixed bug while adding singleton clusters when using -I option, which was uncorrectly adding sequences from excluded taxa | ||
| 12112014: section 'Comparing clusters with external sequence sets' added to manual | ||
| 03122014: fixed bug in download_genomes_ncbi.pl which prevented download of last genome in list in some cases | ||
| 05122014: check input dir/file contains not valid chars ('+') | ||
| 30122014: updated construct_indexes and construct_taxa_indexes | ||
| 09122015: updated format_BLASTN_command to allow blast+ task selection (default is megablast) | ||
| 12012015: updated matchlen to use hash references instead of copies; added simspan_hsps_overlap | ||
| 12012015: updated simspan_hsps to allow calculation with respect to shortest sequence, instead of default (longest) | ||
| 13012015: updated makeIn,makeOr,makeHom to allow coverage calculation with respect to shortest sequence | ||
| 13012015: updated _cluster_makeHomolog.pl, _cluster_makeInparalog.pl, _cluster_makeOrtholog.pl as well | ||
| 13012015: updated find_OMCL_clusters,findAllOrthologiesORTHMCL to allow coverage calculation with respect to shortest sequence | ||
| 13012015: updated format_BLASTN_command,BLASTP,HMMPFAM to use 1CPU, as format_SPLITBLAST_comm,SPLITHMMPFAM control this | ||
| 19012015: fixed bug in add_unmatched_singletons which omitted sequence 1 if it had no hits | ||
| 22012015: added -e to check_BDBHs.pl to get coverage of short sequences if not labelled as full-length ETSs | ||
| 22012015: updated simspan_hsps to allow for subject aligned coords to be in reverse strand | ||
| 26012015: manual updated (FAQS) | ||
| 05022015: shortened gene names derived from 'product' tags in extract_CDSs_from_genbank,_features_from_,_intergenic_from_ | ||
| 05022015: fixed sequence parsing of spliced features in extract_features_from_genbank | ||
| 20022015: fixed bug on -s flag of check_BDBHs.pl | ||
| 20022015: fixed bug affecting -G -I which resulted on singletons from excluded taxa being added to cluster set | ||
| 20022015: fixed bug which incorrectly handled clusters with diverse Pfam compositions as singletons with -D -t 0 | ||
| 20022015: added option -A to get_homologues.pl which computes average identity matrices from blastp/blastn results of clustered sequences | ||
| 25022015: added check to compare_clusters.pl to warn users of forbidden chars on file paths, which caused trouble with embedded R script | ||
| 27022015: fixed weird bug in extract_CDSs_from_genbank that appeared when reading a prokka-delivered gbk files | ||
| 27022015: manual updated and accompanying scripts hcluster_matrix.sh & plot_matrix_heatmap.sh included | ||
| 04032015: added a third arg to marfil_homology::sort_blast_results, a boolean flag stating whether secondary hsps are to be conserved | ||
| 04032015: added global variable $KEEPSCNDHSPS to get_homologues.pl to explicitely state wether secondary hsp are kept (default = 1) | ||
| 11032015: added option -t to check_BDBHs.pl to show only hits from a selected taxon | ||
| 17032015: edited marfil_homology::matrix to save RAM | ||
| 24032015: added %identity to check_BDBHs.pl output | ||
| 24032015: added support in get_homologues for input in the form of a folder of pre-clustered sequences in FASTA format | ||
| 06042015: get_homologues.pl -c now prints the random generator seed | ||
| 09042015: added new accompanying script make_nr_pangenome_matrix.pl | ||
| 13042015: added $MIN_PERSEQID_HOM_EST & $MIN_COVERAGE_HOM_EST to marfil_homology | ||
| 13042015: fixed bug that affected get_homologues -c pangenome re-calculations when $MIN_PERSEQID_HOM & $MIN_COVERAGE_HOM changed | ||
| 30042015: added one-liner for transposing pangenome matrices to compare_clusters.pl and make_nr_pangenome_matrix.pl | ||
| 13052015: added -a to parse_pangenome_matrix.pl to allow finding genes absent in taxa in -B list | ||
| 13052015: added -S to parse_pangenome_matrix.pl to allow filtering out singletons while calling -g or -a | ||
| 29052015: fixed bug while calculating -A average identity matrices | ||
| 07072015: manual updated | ||
| 13082015: added $SOFTCOREFRACTION to marfil_homology.pm and updated parse_pangenome_matrix.pl | ||
| 13082015: added -z to get_homologues to calculate soft-core composition analyses with -c | ||
| 13082015: fixed bug in compare_clusters.pl when file.cluster_list is not in place that produced a pangenome matrix with refs instead of gene occurrences | ||
| 14082015: manual updated | ||
| 03092015: fixed bug in hcluster_matrix.sh when using full path with -i | ||
| 17112015: | ||
| 17112015: ############################################################### | ||
| 17112015: Preparing the move to EST version and git | ||
| 17112015: ############################################################### | ||
| 17112015: | ||
| 17112015: changed BLAST parsing to capture -outfmt 6 'qseqid sseqid pident length qlen slen qstart qend sstart send evalue bitscore' | ||
| 17112015: this implies that old BLAST results from old get_homs releases won't work anymore | ||
| 17112015: %seq_length is only produced with -f; removed this option in -est.pl | ||
| 17112015: removed line id from all_blast.bpo | ||
| 17112015: converted old blastquery to %blastquery[address,total] and eliminated %address_ref | ||
| 17112015: optimized getblock_from_bpofile | ||
| 17112015: changed %gindex to $gindex{tax1}[123,234,tot] | ||
| 17112015: switched %gindex2 by @gindex2 and updated calls in all scripts, including check_BDBHs.pl | ||
| 17112015: handle Evalues as strings when comparing them (eq instead of ==) | ||
| 17112015: added flag_small_clusters, and get_homologues.pl suport -t combined with -c [OMCL|COG] | ||
| 17112015: updated MCL to mcl-14-137 |
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| ## GET_HOMOLOGUES: a versatile software package for pan-genome analysis | ||
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| This software is written and maintained by Bruno Contreras-Moreira (bcontreras _at_ eead.csic.es) and Pablo Vinuesa (vinuesa _at_ ccg.unam.mx). A first version, suitable for analysis of bacterial genomes, was published in: | ||
| This software is written and maintained by Bruno Contreras-Moreira (bcontreras _at_ eead.csic.es) and Pablo Vinuesa (vinuesa _at_ ccg.unam.mx). The first version, **suitable for bacterial genomes**, was described in: | ||
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| Contreras-Moreira,B. and Vinuesa,P. (2013)[Appl.Environ.Microbiol.79:7696-7701](http://aem.asm.org/content/79/24/7696.long) | ||
| [Contreras-Moreira B, Vinuesa P (2013) Appl. Environ. Microbiol. 79:7696-7701](http://aem.asm.org/content/79/24/7696.long) | ||
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| That code has been patched over two years now (see CHANGES), and has recently been adapted to the study of intra-specific eukaryotic pangenomes. We have tested it with whole-genome data and transcripts of grasses. | ||
| That code has been patched over two years now (see CHANGES in each release), and has recently been adapted to the study of **intra-specific eukaryotic pangenomes**. We have tested it with whole-genome data and transcripts of grasses. | ||
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| We kindly ask you to report errors or bugs in the program to the authors and to acknowledge the use of the program in scientific publications. | ||
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| Funding: Fundación ARAID, Consejo Superior de Investigaciones Científicas [grant 200720I038], FEDER [grant CSIC13-4E-2490], DGAPA-PAPIIT UNAM-México [grant IN212010] and CONACyT-México [grants P1-60071 and 179133]. | ||
| *Funding:* Fundación ARAID, Consejo Superior de Investigaciones Científicas [200720I038], FEDER [CSIC13-4E-2490], DGAPA-PAPIIT UNAM-México [IN212010] and CONACyT-México [P1-60071, 179133]. | ||
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