NAME

Bio::Tools::Run::PiseApplication::treealign

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::treealign

      Bioperl class for:

        treealign       phylogenetic alignment of homologous sequences (J. Hein)

        References:

                Hein, J.: Unified approach to alignment and phylogenies. Meth. Enzymol. 183:626-645 (1990).

                Hein, J.: A new method that simultaneously aligns and reconstruct ancestral sequences for any number of homologous sequences, when the phylogeny is given. Mol. Biol. Evol. 6:649-668 (1989). 

                Hein, J.: A tree reconstruction method that is economical in the number of pairwise comparisons used. Mol. Biol. Evol. 6:669-684 (1989). 



      Parameters: 

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


                treealign (String)

                fileseq (Sequence)
                        Sequences File
                        pipe: seqsfile

                seqtype (Excl)
                        Sequence type

                nuseq (Integer)
                        Number of sequences

                gap_open (Integer)
                        Gap open penalty

                gap_ext (Integer)
                        Gap extension penalty

                ancesterout (Switch)
                        Present ancestral sequences

                usertree (Switch)
                        User tree

                usertreefile (InFile)
                        Your tree file

                filetree (OutFile)

                fileali (OutFile)

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/treealign.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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