Ewan Birney

NAME

Bio::Tools::Run::PiseApplication::msa

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::msa

      Bioperl class for:

        MSA     multiple sequence alignment (S. F. Altschul)


      Parameters: 

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


                msa (String)

                seqs (Sequence)
                        Sequences File

                optimal (Switch)
                        Turns off the optimal multiple alignment

                forcedres (InFile)
                        forced aligned residues file (see the documentation)

                endgap (Switch)
                        charges terminal gaps the same as internal gaps

                unweight (Switch)
                        cost = unweighted sum

                maxscore (Integer)
                        maximum score of an optimal multiple alignment

                epsilons (InFile)
                        Epsilons file (see the documentation)

                costs (InFile)
                        Costs file (see the documentation)

                quiet (Switch)
                        suppress verbose output

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/msa.html

  • Bio::Tools::Run::PiseApplication

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

  • Bio::Tools::Run::PiseJob

new

 Title   : new()
 Usage   : my $msa = Bio::Tools::Run::PiseApplication::msa->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::msa 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 $msa = $factory->program('msa');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::msa.