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/wiki/Mailing_lists  - 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 the web:

  http://bugzilla.open-bio.org/

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.