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

NAME
Bio::Tools::Run::PiseApplication::dnapars

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::dnapars

      Bioperl class for:

        Phylip  dnapars - DNA Parsimony 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/dnapars.html
         for available values):

                dnapars (String)

                infile (Sequence)
                        Alignement File
                        pipe: readseq_ok_alig

                use_threshold (Switch)
                        Use Threshold parsimony (T)

                threshold (Integer)
                        Threshold value (if use threshold parsimony)

                use_transversion (Switch)
                        Use Transversion parsimony (N)

                seqboot (Switch)
                        Perform a bootstrap before analysis

                method (Excl)
                        Resampling methods

                seqboot_seed (Integer)
                        Random number seed (must be odd)

                jumble_message (Label)
                        (You may also enter a random number seed for jumble)

                replicates (Integer)
                        How many replicates

                consense (Switch)
                        Compute a consensus tree

                multiple_dataset (String)

                bootconfirm (String)

                bootterminal_type (String)

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

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

                times (Integer)
                        Number of times to jumble

                user_tree (Switch)
                        Use User tree (default: no, search for best tree) (U)

                tree_file (InFile)
                        User Tree file

                weights (Switch)
                        Use weights for sites (W)

                weights_file (InFile)
                        Weights file
                        pipe: phylip_weights

                print_tree (Switch)
                        Print out tree (3)

                print_steps (Switch)
                        Print out steps in each site (4)

                print_sequences (Switch)
                        Print sequences at all nodes of tree (5)

                print_treefile (Switch)
                        Write out trees onto tree file (6)

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

                indent_tree (Switch)
                        Indent treefile

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

                confirm (String)

                terminal_type (String)

                consense_confirm (String)

                consense_terminal_type (String)

                consense_outgroup (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/dnapars.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

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