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

NAME
Bio::Tools::Run::PiseApplication::neighbor

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::neighbor

      Bioperl class for:

        Phylip  neighbor - Neighbor-Joining and UPGMA methods (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/neighbor.html
         for available values):

                neighbor (String)

                distance_method (Excl)
                        Distance method

                infile (InFile)
                        Distances matrix File
                        pipe: phylip_dist

                jumble (Switch)
                        Randomize (jumble) input order (J)

                jumble_seed (Integer)
                        Random number seed for jumble (must be odd)

                multiple_dataset (Switch)
                        Analyze multiple data sets (M)

                datasets_nb (Integer)
                        How many data sets

                multiple_seed (Integer)
                        Random number seed for multiple dataset (must be odd)

                consense (Switch)
                        Compute a consensus tree

                consense_confirm (String)

                consense_terminal_type (String)

                print_tree (Switch)
                        Print out tree (3)

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

                indent_tree (Switch)
                        Indent treefile

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

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

                triangular (Excl)
                        Matrix format

                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
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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/neighbor.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

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