Changes for version 1.13 - 2020-02-02

  • 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
    • Add `Dockerfile`
    • Add `GNUMakefile` target to build docker
    • Put on https:// in rockyb/bpwrapper


Alignment manipulations based on BioPerl
SNP statistics based on BioPerl
Manipulation of FASTA sequences based on BioPerl
Tree manipulations based on BioPerl


command-line utilities for Bio::Perl
Functions for bioaln
Functions for biopop
Functions for bioseq
Functions for biotree