Rechercher une page de manuel
Bio::Tools::Run::PiseApplication::codontree.3pm
Langue: en
Version: 2008-11-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::PiseApplication::codontreeSYNOPSIS
#
DESCRIPTION
Bio::Tools::Run::PiseApplication::codontreeBioperl class for: codontree codon usage table, distance matrix and bases composition (Pesole, Attimonelli and Liuni) References: Graziano Pesole, Marcella Attimonelli and Sabino Liuni (CNR-Bari). NAR (16):5:1988 pp. 1715-1728 Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/codontree.html for available values): codontree (String) seqfile (Sequence) Sequences File tabfile (String) ntable (Excl) Translation table to be used for the computation of distance and codon usage (-NTAble) bc (List) Bases composition to be computed (-BC) eachseq (Switch) Allows the printout of a distinct codon usage table for each sequence of the input file (-EACHseq) dist (Switch) Allows the computation and the printout of the distances matrix (-DISTance) verbose (Switch) Prints on the screen some useful information (-VERbose) bcfile (String) matfile (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/codontree.html
- •
- Bio::Tools::Run::PiseApplication
- •
- Bio::Tools::Run::AnalysisFactory::Pise
- •
- Bio::Tools::Run::PiseJob
new
Title : new() Usage : my $codontree = Bio::Tools::Run::PiseApplication::codontree->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::codontree 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 $codontree = $factory->program('codontree'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::codontree.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre