Bio::Tools::Run::PiseApplication::codontree.3pm

Langue: en

Autres versions - même langue

Version: 2008-11-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

Sommaire

NAME

Bio::Tools::Run::PiseApplication::codontree

SYNOPSIS

   #

DESCRIPTION

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)

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 (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.