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

NAME
Bio::Tools::Run::PiseApplication::seqgen

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::seqgen

      Bioperl class for:

        SeqGen  Sequence-Generator (A. Rambaut, N. C. Grassly)

        References:

                Rambaut, A. and Grassly, N. C. (1996) Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci.

      Parameters:

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

                seqgen (String)

                tree (InFile)
                        Tree File
                        pipe: phylip_tree

                model (Excl)
                        model of nucleotide substitution

                length (Integer)
                        sequence length (-l)

                datasets (Integer)
                        number of simulated datasets per tree (-n)

                scale_branch (Integer)
                        Scale branch lengths  (a decimal number greater > 0) (-s)

                scale_tree (Integer)
                        total tree scale  (a decimal number greater > 0) [default = use branch lengths] (-d)

                rate1 (Integer)
                        rates for codon position heterogeneity, first position (enter a decimal number) (-c)

                rate2 (Integer)
                        rates for codon position heterogeneity, second position (enter a decimal number)

                rate3 (Integer)
                        rates for codon position heterogeneity, third position (enter a decimal number)

                shape (Integer)
                        shape of the gamma distribution to use  with  gamma rate heterogeneity (a decimal  number) (-a)

                categories (Integer)
                        number of categories  for  the  discrete gamma  rate  heterogeneity model (>2 and < 32) (-g)

                freqA (Integer)
                        relative frequencies of the A nucleotide (a decimal number) (-f)

                freqC (Integer)
                        relative frequencies of the C nucleotide (a decimal number)

                freqG (Integer)
                        relative frequencies of the G nucleotide (a decimal number)

                freqT (Integer)
                        relative frequencies of the T nucleotide (a decimal number)

                transratio (Integer)
                        transition transversion ratio (TS/TV) (this is only valid when either the HKY or F84 model has been selected) (-t)

                matrix (String)
                        6 values  for  the general reversable  model's rate matrix (ACTG x ACTG) (REV model), separated by commas (-r)

                phylip (Switch)
                        Relaxed PHYLIP output [default : standard PHYLIP output] (-p)

                quiet (Switch)
                        non verbose output (-q)

                input_seq (Integer)
                        Ancestral Sequence number (-k)

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/seqgen.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

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