Bioperl Release 1.4

Posted on December 23, 2003 by Heikki Lehvaslaiho

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

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