get_homologues-est

This release includes the following updates:

updated BLAST to ncbi-blast-2.16.0+ binaries
test_get_homologues.t now can actually download 8 genomes from NCBI
test_get_homologues.t now includes get_homologues.pl -X (diamond)
improved repository README.md with TOC and links to sections

binaries

Compressed TAR file with binaries to be downloaded after cloning the source repository. This should be done with install.pl

Updated NCBI BLAST+ 2.16.0

get_homologues-est

This release includes the following updates:

• removed .gbk files from test_Streptococcus, should make releases smaller
• added test_Streptococcus and HOWTOTettelin.txt to repo, only in releases before
• updated manuals

get_homologues-est

This release includes the following updates:

• added new script MSA_Ka_Ks.pl to user_utils/dNdS
• added target 'test nonet' to Makefile to allow tests in servers with closed ports
• added parse_pangenome_matrix.pl -R, which modifies -P to control %PAV only for -B
• phyTools::same_sequence_order checks for internal STOP codons in translated sequences
• annotate_cluster.pl fails gracefully when no sequences are read
• annotate_cluster.pl -b -P prints total missense mutations instead of SNPS

get_homologues-est

This release ships with several changes and fixes:

15052023: updated BLAST to faster, smaller ncbi-blast-2.14.0+ binaries
15052022: update install.pl and updated bin.tgz (v3.6)

binaries

Compressed TAR file with binaries to be downloaded after cloning the source repository. This should be done with install.pl

Updated NCBI BLAST+ 2.14.0

get_homologues-est

This release ships with several changes and fixes:

07122022: compare_clusters.pl can intersect clusters from get_pangenes.pl
10032023: check_BDBHs.pl now guesses -i strings literally, escaping special chars
17032023: Release 22-282 of mcl is available, "but MCL itself is unchanged", we'll keep using mcl-14-137
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

get_homologues-est

This release ships with several changes and fixes:

10062022: annotate_cluster.pl -D can now annotate Pfam domains of singleton clusters
10062022: updated .travis.yaml (perl 5.32, libdb-dev, do not apt update)
14062022: compare_clusters.pl can read .cluster_list files from get_pangenes.pl
15062022: added sub same_sequence_order to lib/phyTools.pm
15062022: get_homologues-est.pl now checks that CDS .fna & .faa sequences are in same order
22082022: when checking that .fna & .faa sequences are in same order, CDSs with Ns are skipped
22082022: updated manual-est with description of pangenome matrix versions taken from tutorial

get_homologues-est

This is the first release after publishing GET_HOMOLOGUES and GET_HOMOLOGUES-EST in bioconda

get_homologues-est

This release ships with several changes and fixes:

20042022: added parse_pangenome_matrix.pl -n for matrices that do not include cloud clusters
21042022: transcripts2cdsCPP.pl not tested by default with make test, as bioconda lacks Inline::CPP
21042022: if bin/ not in place phyTools::set_phyTools_env assumes binary dependencies in PATH
21042022: updated install.pl so that it copes with binary dependencies in PATH
21042022: install.pl no_databases COGS only gets/compiles COGS, so that other binaries can be taken from PATH
22042022: added CODE_OF_CONDUCT
28042022: added test_swiss to Makefile
28042022: added compila_conda.pl to bin/COGsoft & added $(CXX) to Makefiles to use in conda recipe (macosx-intel copy still the same)
28042022: COGsoft source released as https://github.com/eead-csic-compbio/get_homologues/releases/download/v3.4.6/COGsoft.tgz
28042022: released updated bin.tgz (v3.5)