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Bio::Tools::Run::PiseApplication::phyml.3pm
Langue: en
Version: 2008-11-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::PiseApplication::phymlSYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::phymlBioperl 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
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- http://bioweb.pasteur.fr/seqanal/interfaces/phyml.html
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- Bio::Tools::Run::PiseApplication
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- Bio::Tools::Run::AnalysisFactory::Pise
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- 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.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre