Bio::Tools::Run::PiseApplication::comalign(3)

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/MailList.shtml  - 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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

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.