NAME

Bio::Tools::Run::PiseApplication::comalign

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::comalign

      Bioperl class for:

        ComAlign        Combining many multiple alignments in one improved alignment (O. Caprani, K. Bucka-Lassen)


      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/comalign.html 
         for available values):


                comalign (String)

                seq (Sequence)
                        Sequences File (-f)
                        pipe: seqsfile

                seed (Integer)
                        Random seed number (-s)

                seqnb (Integer)
                        Number of sequences that are to be aligned (-n)

                iterations (Integer)
                        Number of iterations (-i)

                score (Integer)
                        score: ComAlign records the time it took to  find a solution as good as this score (-l)

                time (Integer)
                        ComAlign marks the best solution found after this number of 1/100 seconds (-t)

                last_iterations (Integer)
                        Makes ComAlign terminate if the score hasn't changed within the last this number of iterations (-c)

                print_best (Switch)
                        Print the best found alignment on termination (-a)

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  http://bugzilla.open-bio.org/

AUTHOR

Catherine Letondal (letondal@pasteur.fr)

COPYRIGHT

Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

SEE ALSO

• http://bioweb.pasteur.fr/seqanal/interfaces/comalign.html

• Bio::Tools::Run::PiseApplication

• Bio::Tools::Run::AnalysisFactory::Pise

• Bio::Tools::Run::PiseJob

new

 Title   : new()
 Usage   : my $comalign = Bio::Tools::Run::PiseApplication::comalign->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::comalign object.
           This method should not be used directly, but rather by 
           a Bio::Tools::Run::AnalysisFactory::Pise instance.
           my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
           my $comalign = $factory->program('comalign');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::comalign.