Bio::Tools::Run::PiseApplication::protpars.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::protpars

SYNOPSIS

   #
 
 

DESCRIPTION

Bio::Tools::Run::PiseApplication::protpars
       Bioperl class for:
 
         Phylip  protpars - Protein Sequence Parcimony Method (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/protpars.html 
          for available values):
 
 
                 protpars (String)
 
                 infile (Sequence)
                         Alignement File
                         pipe: readseq_ok_alig
 
                 use_threshold (Switch)
                         Use Threshold parsimony (T)
 
                 threshold (Integer)
                         Threshold value (if use threshold parsimony)
 
                 code (Excl)
                         Genetic code (U)
 
                 jumble (Switch)
                         Randomize (jumble) input order of sequences (J)
 
                 jumble_seed (Integer)
                         Jumble random number seed (must be odd)
 
                 times (Integer)
                         Number of times to jumble
 
                 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
 
                 consense (Switch)
                         Compute a consensus tree
 
                 user_tree (Switch)
                         Use User tree (default: no, search for best tree) (U)
 
                 tree_file (InFile)
                         User Tree file
 
                 print_tree (Switch)
                         Print out tree (3)
 
                 print_sequences (Switch)
                         Print sequences at all nodes of tree (5)
 
                 print_treefile (Switch)
                         Write out trees onto tree file (6)
 
                 printdata (Switch)
                         Print out the data at start of run (1)
 
                 print_steps (Switch)
                         Print out steps in each site (4)
 
                 indent_tree (Switch)
                         Indent treefile
 
                 outgroup (Integer)
                         Outgroup species (default, use as outgroup species 1) (O)
 
                 confirm (String)
 
                 terminal_type (String)
 
                 multiple_dataset (String)
 
                 bootconfirm (String)
 
                 bootterminal_type (String)
 
                 consense_confirm (String)
 
                 consense_terminal_type (String)
 
                 consense_outgroup (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/protpars.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob

new

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