Bio::BPWrapper 1.15

This release includes a new algorithm for the --trim option in biotree. Also, biopop is temporarily being dropped as a dependency is no longer on CPAN.

Prepping for addition to bioconda

This release removes the dependency on rlib and Bio::Restriction::Analysis (though the later may be re-included later if it ever gets indexed on MetaCPAN). It also includes a new feature to biotree allowing it to re-root on internal nodes. With this version of the module, we hope to make inclusion into Bioconda, and other repositories, much easier.

Other changes include:

• Bumped BioPerl requirement to version 1.7.8
• Bio::DB::Genbank dependency changed to Bio::DB::RefSeq
• XML::DOM::XPath dependency removed
• No longer exports functions using the Bio::Restriction::Analysis module
• Updated the repository URL

release-1.13

• 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

release-1.12

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

Release v1.0

This is release v1.0 of bp-utils. Included are the tools bioaln and bioseq, as well as some tests and a README file. biotree and biopop are not yet ready and so are not included in this file.

Please download the attached bp-utils-release-v1.0.tar.gz file in order to get this release.