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@rocky rocky released this 02 Apr 19:21
· 68 commits to master since this release
release-1.13
98a7213

  • revised for Bio::Perl 1.7.x; uses only Bio::Restriction::Analysis now

  • command options regularized and documentation updated

  • citations and doc links added and updated

  • use Bio::Tools::GuessSeqFormat to guess format in bioaln, bioseq and biopop

  • bioaln:

    • fix bugs in file reading with --concat
    • add ungapped diffs to --pair-diff

  • bioseq:

    • add pick/delete by file
    • add codon-table interface to Tools::Codon::Table and Tools::TUPAC
    • use --gap char - to change "." to "-"a
    • modify --delete to delete by max number of x ambiguous (non-ATCGs) bases
    • modify -t1 to allow non-standard AA to pass (but not internal stops)
    • fix bug in --delete-by-length
    • revive --longest-orf to trim end to be in-frame, add reading frame 1 and -1
    • add --no-revcom (Z)
    • add -codon-info: calculate codon bias of a CDS using Shannon information

  • biotree:

    • Refactor options and update documentation
    • add --add-delete-short-br
    • add --cut-tree: cut tree to identify groups
    • add --pair-diff: pairwise sequence diff
    • add --rename-tips: rename tips accorting to a 2-column table

  • Dockerize

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