[Bioperl-l] Bioperl Release 1.4

[Heikki Lehvaslaiho]

   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
             http://bioperl.org/DIST/current_core_stable.tar.gz
             http://bioperl.org/DIST/current_core_stable.tar.bz2
bioperl-ext  - C compiled extensions
             http://bioperl.org/DIST/current_ext_stable.tar.gz
             http://bioperl.org/DIST/current_ext_stable.tar.bz2
bioperl-run  - wrappers for external programs
             http://bioperl.org/DIST/current_run_stable.tar.gz
             http://bioperl.org/DIST/current_run_stable.tar.bz2


They will also appear shortly at IUBIO mirror 
<http://iubio.bio.indiana.edu/soft/molbio/perl/bioperl/> (later today)
and in CPAN <http://search.cpan.org/dist/bioperl/>.

Remember, all the external modules needed by bioperl-core can be
installed from CPAN under name Bundle-BioPerl
<http://search.cpan.org/dist/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:

   o installable scripts
   o global module version from Bio::Root:Version
   o Bio::Graphics - major improvements; added SVG support
   o Bio::Popgen - population genetics 
   o Bio::Restriction - new restrion analysis modulues
   o Bio::Tools::Analysis - web based DNA and Protein analysis
     framework and several implementaions
   o Bio::Seq::Meta - per residue annotable sequences
   o Bio::Matrix
   o Bio::Matrix::PSM - Position Scoring Matrix
   o Bio::Ontology - major contributions
   o Bio:Tree
   o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA - small inhibitory RNA
   o Bio::SeqFeature::Tools - seqFeature mapping tools, 
     e.g. Bio::SeqFeature::Tools::Unflattener.pm
   o Bio::Tools::dpAlign - pure perl dynamic programming sequence alignment
     (needs Bioperl-ext)
   o new Bio::SearchIO formats
   o new Bio::SeqIO formats: tab, kegg, tigr, game; important fixes for
     old modulues
   o Bio::AlignIO: maf
   o improved Bio::Tools::Genewise
   o Bio::SeqIO now can recognize sequence formats automatically from stream
   o new parsers in Bio::Tools:
      Blat,  Geneid, Lagan, Mdust, Promoterwise, PrositeScan,  
   o several new HOWTOs: SimpleWebAnalysis, Trees, Feature Annotation,
     OBDA Access, Flat Databases
   o 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 at bioperl.org) or the the bioperl bug
tracking system (http://bugzilla.bioperl.org/).


Wishing you all Peaceful Christmas,

        -Heikki and all the bioperl developers