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

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.