Bioperl Release 1.4

The stable Bioperl release 1.4 is available for immediate use at: http://bioperl.org/DIST.

We are releasing simultaneously three modules:

  • bioperl-core - core bioperl modules ( gz b2z)

  • bioperl-ext - C compiled extensions ( gz b2z)

  • bioperl-run - wrappers for external programs ( gz b2z)

They will also appear shortly at the IUBIO mirror (later today) and in CPAN.

Remember, all the external modules needed by bioperl-core can be installed from CPAN under name Bundle-BioPerl.

Changes

Over 3000 file changes have gone into this release since the 1.2 development tree was branched off from the main. These are the main feature enhancements:

  • installable scripts

  • global module version from Bio::Root:Version

  • Bio::Graphics - major improvements; added SVG support

  • Bio::Popgen - population genetics

  • Bio::Restriction - new restrion analysis modulues

  • Bio::Tools::Analysis - web based DNA and Protein analysis framework and several implementaions

  • Bio::Seq::Meta - per residue annotable sequences

  • Bio::Matrix- including Bio::Matrix::PSM - Position Scoring Matrix

  • Bio::Ontology - major contributions

  • Bio:Tree

  • Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA - small inhibitory RNA

  • Bio::SeqFeature::Tools - seqFeature mapping tools, e.g. Bio::SeqFeature::Tools::Unflattener.pm

  • Bio::Tools::dpAlign - pure perl dynamic programming sequence alignment (needs Bioperl-ext)

  • new Bio::SearchIO formats

  • new Bio::SeqIO formats: tab, kegg, tigr, game; important fixes for old modulues

  • Bio::AlignIO: maf

  • improved Bio::Tools::Genewise

  • Bio::SeqIO now can recognize sequence formats automatically from stream

  • new parsers in Bio::Tools: Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,

  • several new HOWTOs: SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat Databases

  • hundreds of new and improved files

For detailed documentation, see individual module documentation in the distribution or in http://doc.bioperl.org/. The tutorials are available at http://bioperl.org/HOWTOs/.

This release is a result of hard work by the bioperl core team, nearly hundred developers and countless suggestions and bug reports at the bioperl mailing list (bioperl-l@bioperl.org) or the the bioperl bug tracking system ( http://bugzilla.bioperl.org/).

Wishing you all Peaceful Christmas,

-Heikki and the bioperl core developers