Linux Certif

Toute la documentation sur la certification Linux LPI

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

NAME

Bio::Tools::Run::PiseApplication::dnapars

SYNOPSIS

   #
 
 

DESCRIPTION

Bio::Tools::Run::PiseApplication::dnapars

       Bioperl class for:
 
         Phylip  dnapars - DNA Parsimony Program (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/dnapars.html 
          for available values):
 
 
                 dnapars (String)
 
                 infile (Sequence)
                         Alignement File
                         pipe: readseq_ok_alig
 
                 use_threshold (Switch)
                         Use Threshold parsimony (T)
 
                 threshold (Integer)
                         Threshold value (if use threshold parsimony)
 
                 use_transversion (Switch)
                         Use Transversion parsimony (N)
 
                 seqboot (Switch)
                         Perform a bootstrap before analysis
 
                 method (Excl)
                         Resampling methods
 
                 seqboot_seed (Integer)
                         Random number seed (must be odd)
 
                 jumble_message (Label)
                         (You may also enter a random number seed for jumble)
 
                 replicates (Integer)
                         How many replicates
 
                 consense (Switch)
                         Compute a consensus tree
 
                 multiple_dataset (String)
 
                 bootconfirm (String)
 
                 bootterminal_type (String)
 
                 jumble (Switch)
                         Randomize (jumble) input order (J)
 
                 jumble_seed (Integer)
                         Random number seed for jumble (must be odd)
 
                 times (Integer)
                         Number of times to jumble
 
                 user_tree (Switch)
                         Use User tree (default: no, search for best tree) (U)
 
                 tree_file (InFile)
                         User Tree file
 
                 weights (Switch)
                         Use weights for sites (W)
 
                 weights_file (InFile)
                         Weights file
                         pipe: phylip_weights
 
                 print_tree (Switch)
                         Print out tree (3)
 
                 print_steps (Switch)
                         Print out steps in each site (4)
 
                 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)
 
                 indent_tree (Switch)
                         Indent treefile
 
                 outgroup (Integer)
                         Outgroup species (default, use as outgroup species 1) (O)
 
                 confirm (String)
 
                 terminal_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

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/dnapars.html

•

Bio::Tools::Run::PiseApplication

•

Bio::Tools::Run::AnalysisFactory::Pise

•

Bio::Tools::Run::PiseJob

new

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