Revision history for Bio::BPWrappers

1.13 2020-02-02:
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* 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:
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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:
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- Another attempt to mollify smokers

1.10 2016-07-01:
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- Adjust testing for MSWin yet again
- More doc improvements

1.08 2016-06-30:
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- Canonicalize biotree -llt output
- More doc updates

1.07 2016-06-30:
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- More complete documentation
- Address GNUMakefile testing issues on CPANTesters

1.06 2016-06-29:
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- 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:
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- 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:
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- First CPAN release.

1.0  2015-02-10:
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- First release. contains two utilities with tests: bioseq & bioaln.
