Bio::Tools::Run::PiseApplication::codontree # Bio::Tools::Run::PiseApplication::codontree Bioperl 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)

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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/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.