$Id: Changes,v 1.4 2003/07/07 15:40:38 heikki Exp $
Revision history for Bioperl run modules

1.2.2 Release update in sync with bioperl core

    o Soaplab
      - API changes
      - binary input added

    o Pise - changes affecting most Bio::Tools::Run:PiseApplication modules
      - Numerous documentation fixes in almost all modules
      - Added code in the SYNOPSIS, as well as the FEEDBACK, COPYRIGHT
        and SEE ALSO parts.
      - the DESCRIPTION section now contains *only* the parameters that
        can be set by the client.
      - remote parameter to -location to conform to
        Bio::Tools::Run::AnalysisFactory interface
      - new programs sirna, tranalign, twofeat (from EMBOSS 2.6).

    o Bio::Tools::Run::Eponine
      - More standardized way of running

    o Bio::Tools::Run::FootPrinter
      - Write the files properly
      - Mark Wagner's enhancements bug #1399

    o Bio::Tools::Run::Genewise
      - more options

    o Bio::Tools::Run::Genscan
      - doc fix

    o Bio::Tools::Run::Hmmpfam
      - Updated to set params properly and return a SearchIO object

    o Bio::Tools::Run::Mdust
      - new location
      - Modified to inherit Bio::Tools::Run::WrapperBase
      - use Bio::Root::IO to build up paths
      - Modified documentation to conform to bioperl format

    o Bio::Tools::Run::Signalp
      - uniform sequence truncation lenght

    o Bio::Tools::Run::Vista
      - new module
      - Support more options
      - More documentation
      - fix reverse sequence bug

    o Bio::Tools::Run::Phylo::Phylip::SeqBoot
      - Allow more than one alignment

    o Bio::Tools::Run::Phylo::Phylip::Neighbor
      - Check for multiple data sets and set parameter accordingly

    o Bio::Tools::Run::Alignment::Blat
      - moved from Bio::Tools::Run name space
      - some code cleanup to avoid warnings and insure filehandles are
        properly closed, etc

    o Bio::Tools::Run::Alignment::Lagan
      - program name included
      - small fixes and addition of options
      - added the right credits.
      - Bio::Tools::Run::Alignment::DBA and Bio::Tools::Run::Alignment::Sim4
      - Quiet declaration warnings


1.2  Developer release

    o Analysis Factory framework- currently providing SOAP access to EMBOSS
      applications

    o Support for FootPrinter, Genewise, Hmmpfam, Primate, Prints,
      Profile, Promoterwise, Pseudowise, Seg, Signalp, Tmhmm,TribeMCL,
      Blat,DBA,Lagan,Sim4,Fasta,ProtML,Vista
    
    o Added support for PHYLIP apps: Consense, DrawGram, DrawTree, SeqBoot

    o Added INSTALL.PROGRAMS providing references to download the program binaries.

    o Bug Fixes that hopefully solves the 'too many open files' problem

0.01 Initial release

    o Package is broken off from bioperl-live to support just
      runnable wrapper modules.

    o Support for PAML codeml tested, aaml still waiting
    
    o Support for Molphy protml, nucml to come

    o Support for EMBOSS pkg - still need to move component from
      bioperl-live Bio::Factory::EMBOSS to this package and 
      rename it Bio::Tools::Run::EMBOSSFactory or something
      equivalent.

    o Support for Clustalw, TCoffee, Local NCBI BLAST.
    
    o RepeatMasker, Genscan, Pseudowise, TribeMCL, Primate, Eponine.
    
    o Support for remote analysis through Pise and NCBI Web Blast
      queue.

    o Select PHYLIP apps: Neighbor, ProtDist, and ProtPars.