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

NAME
Bio::Tools::Run::PiseApplication::protdist

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::protdist

      Bioperl class for:

        Phylip  protdist - Program to compute distance matrix from protein sequences (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/protdist.html
         for available values):

                protdist (String)

                infile (Sequence)
                        Alignement File
                        pipe: readseq_ok_alig

                method (Excl)
                        Distance model (P)

                gamma_dist (Excl)
                        Gamma distribution of rates among positions (G)

                seqboot (Switch)
                        Perform a bootstrap before analysis

                resamp_method (Excl)
                        Resampling methods

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

                replicates (Integer)
                        How many replicates

                weights (Switch)
                        Use weights for sites (W)

                weights_file (InFile)
                        Weights file

                multiple_dataset (String)

                bootconfirm (String)

                bootterminal_type (String)

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

                code (Excl)
                        Genetic code (U)

                categorization (Excl)
                        Categorization of amino acids (A)

                change_prob (Integer)
                        Prob change category (1.0=easy) (E)

                ratio (Integer)
                        Transition/transversion ratio (T)

                base_frequencies (Integer)
                        Base frequencies for A, C, G, T/U (separated by commas)

                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/protdist.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

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