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Bio::Tools::Run::PiseApplication::seqgen.3pm

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)
 
                 partition_numb (Integer)
                         Number of partitions for each dataset (-p)
 
                 scale_branch (Float)
                         Scale branch lengths  (a decimal number greater > 0) (-s)
 
                 scale_tree (Float)
                         total tree scale  (a decimal number greater > 0) [default = use branch lengths] (-d)
 
                 rate1 (Float)
                         rates for codon position heterogeneity, first position (enter a decimal number) (-c)
 
                 rate2 (Float)
                         rates for codon position heterogeneity, second position (enter a decimal number)
 
                 rate3 (Float)
                         rates for codon position heterogeneity, third position (enter a decimal number)
 
                 shape (Float)
                         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)
 
                 invar_site (Float)
                         proportion of sites that should be invariable (a real         number >= 0.0 and < 1.0) (-i)
 
                 freqA (Float)
                         relative frequencies of the A nucleotide (a decimal number) (-f)
 
                 freqC (Float)
                         relative frequencies of the C nucleotide (a decimal number)
 
                 freqG (Float)
                         relative frequencies of the G nucleotide (a decimal number)
 
                 freqT (Float)
                         relative frequencies of the T nucleotide (a decimal number)
 
                 transratio (Float)
                         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)
 
                 random_seed (Integer)
                         random number seed (-z)
 
                 phylip (Excl)
                         output file format [default : standard PHYLIP output]
 
                 quiet (Switch)
                         non verbose output (-q)
 
                 write_ancest (Switch)
                         write the ancestral sequences (-wa)
 
                 write_sites (Switch)
                         write the sites rates (-wr)
 
                 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/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/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.