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Bio::Tools::Run::PiseApplication::Puzzle.3pm
Langue: en
Version: 2008-11-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::PiseApplication::PuzzleSYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::PuzzleBioperl class for: Puzzle Tree reconstruction for sequences by quartet puzzling and maximum likelihood (Strimmer, von Haeseler) References: Strimmer, K., and A. von Haeseler. 1996. Quartet puzzling:A quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13: 964-969. Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/Puzzle.html for available values): Puzzle (String) stdinput (String) confirm (String) infile (Sequence) Alignement File pipe: readseq_ok_alig seqtype (Excl) Is it a DNA or protein sequence approximate (Switch) Approximate quartet likelihood (v) puzzling_step (Integer) Number of puzzling steps (n) protein_model (Excl) Model of substitution for protein (if no automatic guess) (m) ratio (Float) Transition/transversion ratio (t) GTR_acrate (Float) A-C rate (1) GTR_agrate (Float) A-G rate (2) GTR_atrate (Float) A-T rate (3) GTR_cgrate (Float) C-G rate (4) GTR_ctrate (Float) C-T rate (5) GTR_gtrate (Float) G-T rate (6) use_specified (Switch) Use specified values a_freq (Float) pi(A) c_freq (Float) pi(C) g_freq (Float) pi(G) dna_model (Excl) Model of substitution for DNA (m) constrain_TN (Switch) Constrain TN model to F84 model (p) f84_ratio (Float) Expected F84 Transition/transversion ratio y_r (Float) Y/R transition parameter (r) symmetrize_frequencies (Switch) Symmetrize doublet frequencies (s) rate_heterogeneity (Excl) Model of rate heterogeneity (w) alpha (Float) Gamma distribution parameter alpha (a) gamma_number (Integer) Number of Gamma rate categories (c) invariable (Float) Fraction of invariable sites (i) user_tree (Switch) Tree search procedure: User tree (k) tree_file (InFile) User Tree file no_tree (Switch) Pairwise distances only (no tree) (k) outgroup (Integer) Display as outgroup (o) branch_length (Switch) Compute clocklike branch lengths (z) estimates (Excl) Parameter estimates (e) estimation_by (Excl) Parameter estimation by (x) list_unresolved (Switch) List unresolved quartets (u) list_trees (Switch) List puzzling step trees (j)
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/Puzzle.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 $Puzzle = Bio::Tools::Run::PiseApplication::Puzzle->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::Puzzle 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 $Puzzle = $factory->program('Puzzle'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::Puzzle.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre