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://https://hub.docker.com in rockyb/bpwrapper
Documentation
Alignment manipulations based on BioPerl
SNP statistics based on BioPerl
Manipulation of FASTA sequences based on BioPerl
Tree manipulations based on BioPerl
Modules
command-line utilities for Bio::Perl
Functions for bioaln
Functions for biopop
Functions for bioseq
Functions for biotree