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Revision history for Bio::BPWrappers
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
1.12 2017-07-15:
----------------
bioaln:
- Allow BLAST input in bioaln
biotree:
- make biotree -m more efficent by avoiding pair-wise
OTU distances
- Add options:
--label-selected-nodes
--del-low-boot
--mid-point
--as-text
- change option --distance to --dist
Bio::BPWrapper::SeqManipulations:
- Added support for IUPAC codes
- Added support for multimple sequence files
when performing restriction analyses
Correct and expand documentation, add PDF reference
1.11 2016-07-01:
----------------
- Another attempt to mollify smokers
1.10 2016-07-01:
----------------
- Adjust testing for MSWin yet again
- More doc improvements
1.08 2016-06-30:
----------------
- Canonicalize biotree -llt output
- More doc updates
1.07 2016-06-30:
----------------
- More complete documentation
- Address GNUMakefile testing issues on CPANTesters
1.06 2016-06-29:
----------------
- Canonicalize bioaln --avpid floating point values
- Convert links from rocky to bioperl github namespace
- Start documenting Bio::BPWrapper::SeqManipulations
- Changes to decrease likelihood automated test failures
- misc doc changes
1.05 2016-06-28:
----------------
- Try to addess OSX testing problems:
test using long options
- Start package documentation:
Bio::BPWrapper::AlnManipulations
- improve/standardize command-line documentation
1.04 2016-06-02:
- revise bioaln documentation
- force at least Perl 5.10 on CPAN install
1.03 2016-06-01:
----------------
- Make behavior the same across more Platforms:
use a bundled Getopt::Long. This addresses
the majority of install problems we see on CPAN
- Revise bioseq doc
1.01 2016-05-26:
----------------
- First CPAN release.
1.0 2015-02-10:
----------------
- First release. contains two utilities with tests: bioseq & bioaln.