Bioperl 1.2.2 released

This is a bug fix release from the stable branch.

The Bioperl release 1.2.2 is available at

and is propagating around CPAN now.

Bioperl-run is a collection of modules that wrap bioinformatics
applications to allow running them from bioperl. The release cycle of
bioperl-run follows the core. The latest bioperl-run release is
therefore at:

The main bug fixes in this release are:


  • OBDA Registry code is up to latest specs and fuly functional
  • Sequence retrieval from NCBI works again after URL change

  • The BLAST output parsed now works on megablast and parses
    even the last hit

  • Result writers now correctly report alignment start/end info
    for translated BLAST/FASTA searches

  • Improvements in closing and keeping open file handles
  • Robustness of Bio::Graphics modules have been improved
  • Other improved modules:
    • Bio::OntologyIO::dagflat
    • Bio::Annotation::OntologyTerm
    • Bio::TreeIO::newick
    • Bio::Tools::BPbl2seq
    • Bio::Tools::Genemark
    • Bio::SeqIO::genbank


  • SoapLab and PISE improvements
  • New wrapper for Vista:


  • Other improved modules:
    • Bio::Tools::Run::Eponine
    • Bio::Tools::Run::FootPrinter
    • Bio::Tools::Run::Genewise
    • Bio::Tools::Run::Genscan
    • Bio::Tools::Run::Hmmpfam
    • Bio::Tools::Run::Mdust
    • Bio::Tools::Run::Signalp
    • Bio::Tools::Run::Phylo::Phylip::SeqBoot
    • Bio::Tools::Run::Phylo::Phylip::Neighbor
    • Bio::Tools::Run::Alignment::Blat
    • Bio::Tools::Run::Alignment::Lagan

More details are in distribution file ‘Changes’.

Thank you for all who reported bugs and made this release possible.