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 listsReporting 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.