Bioperl Release 1.4

The stable Bioperl release 1.4 is available for immediate use at:

We are releasing simultaneously three modules:

  • bioperl-core – core bioperl modules (



  • bioperl-ext – C compiled extensions (



  • bioperl-run – wrappers for external programs (



They will also appear shortly at

the IUBIO mirror
(later today)
and in

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



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,

  • 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 The tutorials are
available at

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 ( or the the bioperl bug
tracking system (

Wishing you all Peaceful Christmas,

-Heikki and the bioperl core developers