Bio::Tools::Run::PiseApplication::seqgen # 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)

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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.bioperl.org/ Catherine Letondal (letondal@pasteur.fr) 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. This software is provided "as is" without warranty of any kind. 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.