Get Homologues Versions Save

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

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)

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

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

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

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

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)

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

COGsoft/*/Makefile in bin.tgz now have $(CXX) instead of g++

This is the COGtriangles code with minor include tweaks so that it compiles in conda. Running $ perl conda_compile.pl creates new binaries and puts them in bin/

The original code can be obtained from https://ftp.ncbi.nih.gov/pub/wolf/COGs/COGsoft/ https://sourceforge.net/projects/cogtriangles/

Please see Readme.2012.04.txt for credits and terms of use.

This release ships with several changes and fixes:

16092021: updated hcluster_pangenome_matrix.sh: added functions cleanup_R_script & print_version; checked and fixed options and associated names; added options -v, -h; improved output file checking; 100% check compliance 05112021: added explanation to annotate_cluster.pl regarding MVIEW non-reported deletions in longest sequences 05112021: improved manual description of MVIEW alignments within annotate_cluster.pl 05112021: compare_clusters.pl now prints all duplicated clusters to duplicated.cluster_list ; explained in manual 08112021: updated manual/HOWTOsge.txt 03122021: genbank files produced by PATRIC/RAST2 can now be parsed (thanks Irene Ortega!) 09122021: updated format_BLAST[NP]_command_aligns to take a max number of hits to report, 09212021: this fixes a bug in annotate_clusters.pl that affected clusters > 250 seqs (thanks carolynzi!) 22122021: made %feature_output non-redundant 15022022: make_nr_pangenome_matrix.pl now produces logfile to see date of redundant sequences (thanks carolynzi!) 21022022: updated transpose oneliner in make_nr_pangenome_matrix.pl (thanks carolynzi!) 23022022: make_nr_pangenome_matrix.pl now logs recursive list of redundant clusters (thanks carolynzi!) 23022022: get_homologues.pl stops if no input sequences are parsed and remined accepted extensions (thanks apoorva004!) 28022022: removed unused vars from lib/marfil_homology.pm (thanks https://metacpan.org/pod/App::perlvars) 09032022: annotate_cluster.pl stops if < 2 sequences 16032022: parse_pangenome_matrix.pl can read pangene_matrix.tab produced at https://github.com/Ensembl/plant-scripts/tree/master/pangenes 17032022: format_BLASTN_command_aligns now takes only one 1hsp per query (thanks carolynzi!) 17032022: annotate_cluster.pl now prints the name of longest sequence 05042022: updated TODO