Bio::Tools::Run::PiseApplication::kitsch.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::kitsch

SYNOPSIS

   #
 
 

DESCRIPTION

Bio::Tools::Run::PiseApplication::kitsch
       Bioperl class for:
 
         Phylip  kitsch - Fitch-Margoliash and Least Squares Methods with Evolutionary Clock (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/kitsch.html 
          for available values):
 
 
                 kitsch (String)
 
                 infile (InFile)
                         Distances matrix File
                         pipe: phylip_dist
 
                 method (Excl)
                         Program method
 
                 negative_branch (Switch)
                         Negative branch lengths allowed (-)
 
                 power (Integer)
                         Power (P)
 
                 jumble (Switch)
                         Randomize (jumble) input order (J)
 
                 jumble_seed (Integer)
                         Random number seed (must be odd)
 
                 times (Integer)
                         Number of times to jumble
 
                 multiple_dataset (Switch)
                         Analyze multiple data sets (M)
 
                 datasets_nb (Integer)
                         How many data sets
 
                 consense (Switch)
                         Compute a consensus tree
 
                 consense_confirm (String)
 
                 consense_terminal_type (String)
 
                 user_tree (Switch)
                         Use User tree (default: no, search for best tree) (U)
 
                 tree_file (InFile)
                         User Tree file
 
                 tree_nb (Integer)
                         How many tree(s) in the User Tree file
 
                 print_tree (Switch)
                         Print out tree (3)
 
                 print_treefile (Switch)
                         Write out trees onto tree file (4)
 
                 printdata (Switch)
                         Print out the data at start of run (1)
 
                 indent_tree (Switch)
                         Indent treefile
 
                 triangular (Excl)
                         Matrix format
 
                 confirm (String)
 
                 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/kitsch.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob

new

  Title   : new()
  Usage   : my $kitsch = Bio::Tools::Run::PiseApplication::kitsch->new($location, $email, @params);
  Function: Creates a Bio::Tools::Run::PiseApplication::kitsch 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 $kitsch = $factory->program('kitsch');
  Example : -
  Returns : An instance of Bio::Tools::Run::PiseApplication::kitsch.