get_homologues-est

Release 09062017 (v3.0.5) ships with the following changes:
parse_pangenome_matrix.pl -I now supports -B to produce lists of absent genes in pan-genome matrix subsets
added message to make_nr_pangenome_matrix.pl to warn users that BLAST files must be removed with different refs
added option -r to annotate_cluster.pl so that external sequences can be used to drive cluster alignment
updated lib/ForkManager.pm to v1.19 [http://search.cpan.org/perldoc?Parallel%3A%3AForkManager]
fixed bug in get_homologues.pl -X which produced zero clusters when new sequences files were added to previous results

get_homologues-est

18042017 (v3.0.4) ships with a few minor fixes:
updated complete and WGS genome downloads in download_genomes_ncbi.pl
updated FAQ about computing bootstrap values of parsimony pangenome trees
updated LICENSE
added parse_pangenome_matrix.pl -I to produce reports for subsets of taxa in a pangenome matrix
parse_pangenome_matrix.pl -s now produces the number of cloud, shell & core clusters per taxon
fixed uniprot ftp time-out error message in install.pl (thanks hliang)

get_homologues-est

20170302 (v3.0.3) fixes a bug that affected parse_pangenome_matrix.pl -p and updates the manual section with instructions for optionally installing a Grid Engine queue management system in a multi-core box.

get_homologues-est

20170208 (v3.0.2) is the first release after acceptance of the paper describing the GET_HOMOLOGUES-EST algorithms, which you can read at http://journal.frontiersin.org/article/10.3389/fpls.2017.00184/full.

get_homologues-est

20170105 (v3.0.1) is the first release of version 3, with new features in both get_homologues.pl:

22122016: added DIAMOND blastp support in phyTools.pm and marfil_homology.pm
22122016: updated lib/est/transcripts.pm after adding added DIAMOND blastp
28122016: extract_*_genbank subs in lib/phyTools.pm now can read GZIP- or BZIP2-compressed input files
28122016: get_homologues.pl can now take GZIP- or BZIP2-compressed input files
30122016: note: compressed multi-contig gbk files produce FASTA files with different seq order
30122016: added DIAMOND blastp to get_homologues.pl, which can be called with -X
30122016: compare_clusters.pl now correctly shortens DIAMOND cluster dirs
05012017: updated manuals and added E.coli -X benchmark

and get_homologues-est.pl:

20122016: added table with transcript2cds benchmark to EST manual
20122016: added option --more-sensitive to DIAMOND in lib/est/transcripts.pm
05012017: updated $BATCHSIZE to 1000 in get_homologues-est.pl

get_homologues-est

Added DIAMOND to transcripts2CDS*.pl which can be used to speed up ORF finding.

get_homologues-est

This is release 27102016 (v2.0.22) which fixes a bug in plot_matrix_heatmap.sh -c X and now only rows with values < X are retained, as expected

get_homologues-est

This is release 18102016 (v2.0.21) of GET_HOMOLOGUES, which improves handling of duplicated sequences in pfam_enrich.pl and updates the manual.

get_homologues-est

This is release 20092016 (v2.0.20) of GET_HOMOLOGUES, which ships with a few fixed bugs and a new example in the EST manual, which describes the steps required to compute Pfam enrichment of a set of clusters.

get_homologues-est

This is release 02082016 (v2.0.19) of GET_HOMOLOGUES, which ships with updated lib/phyTools subroutines (extract_intergenic_from_genbank & extract_CDSs_from_genbank) to cope with GenBank files produced with RAST, which might not have a protein_id not locus_tag, but will have a SEED:fig|xxxx.yyyy.zzzz code.