Rechercher une page de manuel
Bio::Tools::Run::PiseApplication::dnadist.3pm
Langue: en
Version: 2008-11-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::PiseApplication::dnadistSYNOPSIS
#
DESCRIPTION
Bio::Tools::Run::PiseApplication::dnadistBioperl class for: Phylip dnadist - Compute distance matrix from nucleotide sequences (Felsenstein) References: Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle. Felsenstein, J. 1989. PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166. Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/dnadist.html for available values): dnadist (String) infile (Sequence) Alignment File pipe: readseq_ok_alig distance (Excl) Distance (D) ratio (Integer) Transition/transversion ratio (T) gamma (Excl) Gamma distributed rates across sites (G) variation_coeff (Float) Coefficient of variation of substitution rate among sites (must be positive) (if Gamma) invariant_sites (Float) Fraction of invariant sites (if Gamma) empirical_frequencies (Switch) Use empirical base frequencies (F) base_frequencies (String) Base frequencies for A, C, G, T/U (if not empirical) (separated by commas) one_category (Switch) One category of substitution rates (C) n_categ (Integer) Number of categories (1 to 9) categ_rates (String) Rate for each category (separated by commas) weights (Switch) Use weights for sites (W) weights_file (InFile) Weights file seqboot (Switch) Perform a bootstrap before analysis method (Excl) Resampling methods seqboot_seed (Integer) Random number seed (must be odd) replicates (Integer) How many replicates matrix_form (Switch) Lower-triangular distance matrix (L) printdata (Switch) Print out the data at start of run (1) confirm (String) terminal_type (String) multiple_dataset (String) seqboot_confirm (String) seqboot_terminal_type (String)
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/dnadist.html
- •
- Bio::Tools::Run::PiseApplication
- •
- Bio::Tools::Run::AnalysisFactory::Pise
- •
- Bio::Tools::Run::PiseJob
new
Title : new() Usage : my $dnadist = Bio::Tools::Run::PiseApplication::dnadist->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::dnadist 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 $dnadist = $factory->program('dnadist'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::dnadist.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre