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