NAME

Bio::Tools::Run::PiseApplication::dca

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::dca

      Bioperl class for:

        DCA     Divide-and-Conquer Multiple Sequence Alignment (J. Stoye)

        References:

                A.W.M. Dress, G. Füllen, S.W. Perrey, A Divide and Conquer Approach to Multiple Alignment, Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology (ISMB 95), AAAI Press, Menlo Park, CA, USA, 107-113, 1995.

                J. Stoye, Multiple Sequence Alignment with the Divide-and-Conquer Method, Gene 211(2), GC45-GC56, 1998. (Gene-COMBIS)



      Parameters: 

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


                dca (String)

                seq (Sequence)
                        Sequences File
                        pipe: seqsfile

                cost (Excl)
                        Cost matrix (default: depends on sequences) (-c)

                gaps (Switch)
                        Penalize end gaps as internal gaps (default: free shift) (-g)

                approximate (Switch)
                        Use approximate cut positions (-a)

                intensity (Float)
                        Weight intensity (-b)

                recursion (Integer)
                        Recursion stop size (-l)

                window (Integer)
                        Window size (-w)

                quiet (Switch)

                output_format (Excl)
                        Output format (-f)

                suppress_output (Switch)
                        Suppress output about progress of the program (-o)

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/dca.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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