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

NAME
Bio::Tools::Run::PiseApplication::consense

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::consense

      Bioperl class for:

        Phylip  consense - Consensus tree program (Felsenstein)

        References:

                Felsenstein, J.  1993.  PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author.  Department of Genetics, University of Washington, Seattle.

                Felsenstein, J.  1989.  PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics  5: 164-166.

      Parameters:

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

                consense (String)

                infile (InFile)
                        Trees File
                        pipe: phylip_tree

                type (Excl)
                        Consensus type

                print_tree (Switch)
                        Print out tree (3)

                print_treefile (Switch)
                        Write out trees onto tree file (4)

                printdata (Switch)
                        Print out the data at start of run (1)

                indent_tree (Switch)
                        Indent treefile

                outgroup (Integer)
                        Outgroup (default, use as outgroup species 1) (O)

                rooted (Switch)
                        Trees to be treated as rooted

                confirm (String)

                terminal_type (String)

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/consense.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

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