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

NAME
Bio::Tools::Run::PiseApplication::clique

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::clique

      Bioperl class for:

        Phylip  clique - Compatibility 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/clique.html
         for available values):

                clique (String)

                infile (InFile)
                        Input File

                use_ancestral_state (Switch)
                        Use ancestral states in input file (A)

                spec_min_clique_size (Switch)
                        Specify minimum clique size? (C)

                min_clique_size (Integer)
                        Minimum clique size

                multiple_dataset (Switch)
                        Analyze multiple data sets (M)

                datasets_nb (Integer)
                        How many data sets

                consense (Switch)
                        Compute a consensus tree

                print_matrix (Switch)
                        Print out compatibility matrix (3)

                print_tree (Switch)
                        Print out tree (4)

                print_treefile (Switch)
                        Write out trees onto tree file (5)

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

                indent_tree (Switch)
                        Indent treefile

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

                confirm (String)

                terminal_type (String)

                consense_confirm (String)

                consense_terminal_type (String)

FEEDBACK

  Mailing Lists
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  bioperl-l@bioperl.org              - General discussion
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  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/clique.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

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