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@eead-csic-compbio eead-csic-compbio released this 24 May 11:28
· 319 commits to master since this release
v3.1.2
ee1b865

These are the relevant updates release 20180524 (v3.1.2):

  • sequences longer than $MAXSEQLENGTH are skipped (by default $MAXSEQLENGTH=25kb)
  • compare_clusters.pl -m now produces also pangenome_genes file listing sequences names in each cluster
  • compare_clusters.pl -m now sorts taxon names when printing pangenome matrices
  • added -P option to compute perc of conserved proteins (POCP) in get_homologues.pl
  • added -P option to compute perc of conserved sequences (POCS) in get_homologues-est.pl
  • simplified headers in output FASTA files of get_homologues-est down to: >first_non-blank_word [source_taxon.fna]
  • modified phyTools::check_variants_FASTA_alignment to compute also private variants if listsA & B are passed
  • annotate_cluster.pl now can take -A/-B lists of taxa to compute private variants in the aligned sequences of the cluster
  • updated descriptions of annotate_cluster.pl in manuals
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