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

NAME
Bio::Tools::Run::PiseApplication::protpars

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::protpars

      Bioperl class for:

        Phylip  protpars - Protein Sequence Parcimony Method (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/protpars.html
         for available values):

                protpars (String)

                infile (Sequence)
                        Alignement File
                        pipe: readseq_ok_alig

                use_threshold (Switch)
                        Use Threshold parsimony (T)

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

                code (Excl)
                        Genetic code (U)

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

                jumble_seed (Integer)
                        Jumble random number seed (must be odd)

                times (Integer)
                        Number of times to jumble

                seqboot (Switch)
                        Perform a bootstrap before analysis

                method (Excl)
                        Resampling methods

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

                replicates (Integer)
                        How many replicates

                consense (Switch)
                        Compute a consensus tree

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

                tree_file (InFile)
                        User Tree file

                print_tree (Switch)
                        Print out tree (3)

                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)

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

                indent_tree (Switch)
                        Indent treefile

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

                confirm (String)

                terminal_type (String)

                multiple_dataset (String)

                bootconfirm (String)

                bootterminal_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/protpars.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

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