NAME

Bio::Tools::Run::PiseApplication::phyml

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::phyml

      Bioperl class for:

        PHYML   a program that  computes maximum likelihood phylogenies from DNA or AA homologous sequences (S. Guindon and O. Gascuel)

        References:

                 Guindon, S. and Gascuel, O. (2003) A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood Syst. Biol., 52, 696-704



      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/phyml.html 
         for available values):


                phyml (String)

                alignment (Sequence)
                        Sequence Alignment
                        pipe: readseq_ok_alig

                data_type (Excl)
                        Data type

                format (Excl)
                        Format

                datasets (Integer)
                        Number of data sets to analyse

                bootstrap_sets (Integer)
                        Number of bootstraps sets to analyse (only works with one data set to analyse)

                model (Excl)
                        Substitution model

                kappa (Float)
                        Transition/transversion ratio (only for DNA sequences)

                kappa_e (Switch)
                        Estimate Transition/transversion ratio? (only for DNA sequences)

                invar (Float)
                        Proportion of invariable sites

                invar_e (Switch)
                        Estimate proportion of invariable sites?

                nb_categ (Integer)
                        number of relative substitution rate categories (ex:4)

                alpha (Float)
                        Gamma distribution parameter

                alpha_e (Switch)
                        Estimate Gamma distribution parameter?

                opt_topology (Switch)
                        Optimise tree topology?

                opt_lengths (Switch)
                        Optimise branch lengths and rate parameters?

                user_tree (Switch)
                        Starting tree?

                user_tree_file (InFile)
                        Starting tree filename (Newick format)
                        pipe: phylip_tree

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/phyml.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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