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

Langue: en

Autres versions - même langue

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

Section: 3 (Bibliothèques de fonctions)

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/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/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.