Bio::Tools::Run::PiseApplication::dnadist(3)

NAME
Bio::Tools::Run::PiseApplication::dnadist

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::dnadist

      Bioperl 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/MailList.shtml  - 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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

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.