get_homologues-est

This is release 12072016 (v2.0.18) of GET_HOMOLOGUES, which ships with updated lib/phyTools sub find_COGs to limit coverage cutoff to 99% when using COGS algorithm (-G).

get_homologues-est

This is release 23062016 (v2.0.17) of GET_HOMOLOGUES, which ships with updated lib/phyTools subroutines (extract_intergenic_from_genbank & extract_CDSs_from_genbank) to cope with the announced deprecation of GI codes at GenBank: https://www.ncbi.nlm.nih.gov/news/03-02-2016-phase-out-of-GI-numbers

get_homologues-est

This is release 27052016 (v2.0.16) of GET_HOMOLOGUES, which ships with a few fixes:

• added global $INCLUDEORDER to get_homologues-est.pl to control wheter -c analyses should follow -I include order
  • parse_pangenome_matrix.pl now can parse non-redundant pangenome matrices made with make_nr_pangenome_matrix.pl
• parse_pangenome_matrix.pl barplot colors can now be encoded in RGB scale in variable %RGBCOLORS
• removed warnings when options -f/-P not invoked in make_nr_pangenome_matrix.pl
• added -e to reference matching in make_nr_pangenome_matrix.pl
• updated manual-est with transcript2CDS description
• added degenerate DNA bases [WSRYKM] to make_nr_pangenome_matrix.pl
• increased hit number while matching reference sequences in make_nr_pangenome_matrix.pl
• make_nr_pangenome_matrix.pl can now take all references matching nr clusters (see var $ONLYBESTREFHIT)
• improved the description of $MIN_PERSEQID_HOM_EST and $MIN_COVERAGE_HOM_EST and added a FAQ
• improved the description of $MIN_PERSEQID_HOM and $MIN_COVERAGE_HOM and added a FAQ

get_homologues-est

This is release 05052016 (v2.0.15) of GET_HOMOLOGUES, which ships with a few fixes, the last two important ones:

• added check so that initial core/pan size cannot be < 0 (get_homologues-est.pl)
• added option -c to plot_matrix_heatmap.sh to filter out excessive redundancy by imposing a max identity cut-off value
• set $MIN_PERSEQID_HOM_EST=70 and $MIN_COVERAGE_HOM_EST=50 in lib/marfil_homology.pm
• added new figures to manual_get_homologues-est.pdf
• fixed bug in get_homologues-est.pl -c so that redundant isoforms are not added to pan/core sets
• fixed bug in get_homologues.pl -c so that inparalogues are substracted while adding up novel BDBH pan-genome genes

get_homologues-est

This is release 12042016 (v2.0.14) of GET_HOMOLOGUES, which ships with a few fixes:

08042016: fixed logging of -c core/pan-genome sizes when using -M/-G
11042016: updated marfil_homology::flag_small_clusters
12042016: edited get_homologues-est.pl -M -c -t taxa so that initial core/pan size only considers clusters with occupancy >= min_taxa
12042016: marfil_homology::makeIsoform now prints taxon name to help detect problematic datasets or incomplete BLAST jobs
12042016: added option -a to plot_pancore_matrix.pl to generate snapshots of pangenome size simulations
PS:
13042016: added check so that initial core/pan size cannot be < 0 (get_homologues-est.pl)

get_homologues-est

This is release 31032016 (v2.0.13) of GET_HOMOLOGUES, which ships with a few fixes:

1. parse_pangenome_matrix.pl now prints -P & -S values to pangenes_list.txt
2. parse_pangenome_matrix.pl barplots produced with -s have longer Y-axes, which can now be controlled with global $YLIMRATIO
3. get_homologues manual updated, including figures 12 & 13
4. marfil_homology::find_COGs made faster after trimming a couple of regexes and replacing grep with (first)[http://perldoc.perl.org/List/Util.html#first], thanks Andre Luiz de Oliveira!
5. updated test_Streptococcus/test_Streptococcus_download_list.txt
6. FAQ added to get_homologues-est manual

get_homologues-est

This is release 23032016 (v2.0.12) of GET_HOMOLOGUES, which fixes parse_pangenome_matrix.pl so that it checks that taxon names in -A/-B lists match those in input pangenome_matrix.tab.

get_homologues-est

This is release 11032016 (v2.0.11) of GET_HOMOLOGUES, which adds new script pfam_enrich,pl to calculate enrichment of Pfam domains between two sets of sequence clusters.

get_homologues-est

This is release 26022016 (v2.0.10) of GET_HOMOLOGUES, which adds annotate_cluster.pl as an auxiliary script and updates several other scripts and manuals. This is the first release that ships with mview.

get_homologues-est

This is release 23022016 (v2.0.9) of GET_HOMOLOGUES, which fixes the way compare_clusters.pl sorts intergenic clusters and updates default -S value for get_homologues-est.pl, which is now 95%