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

Langue: en

Autres versions - même langue

Version: 2005-10-09 (mandriva - 01/05/08)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::Run::PiseApplication::lvb

SYNOPSIS

   #
 
 

DESCRIPTION

Bio::Tools::Run::PiseApplication::lvb
       Bioperl class for:
 
         LVB     Reconstructing Evolution With Parsimony And Simulated Annealing (D. Barker)
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/lvb.html 
          for available values):
 
 
                 lvb (String)
 
                 infile (Sequence)
                         Alignement File
                         pipe: readseq_ok_alig
 
                 convert (Switch)
                         Convert the alignment file to LVB format
 
                 method (Excl)
                         Search method (method)
 
                 seed (Integer)
                         Seed for the random number generator (seed)
 
                 t0 (Float)
                         Initial temperature (0 < t0 <= 1.0) (t0)
 
                 t1 (Float)
                         Second temperature (0 < t1 <= 1.0 and t1 < t0) (t1)
 
                 maxaccept (Integer)
                         How many new trees are accepted (maxaccept)
 
                 maxpropose (Integer)
                         How many changes are proposed (maxpropose)
 
                 maxfail (Integer)
                         How many 'failed' successive temperatures to allow (maxfail)
 
                 equivalent (Excl)
                         Equivalent characters sets (equivalent)
 
                 matchchar (Switch)
                         Mark similar characters relative to the first row by a dot (matchchar)
 
                 ignorechars (Excl)
                         Ignore characters containing (ignorechars)
 
                 outgroup (String)
                         Name of the outgroup (outgroup)
 
                 runs (Integer)
                         Number of runs (runs)
 
                 verbose (Switch)
                         Statistics (verbose)
 
                 titleprec (Switch)
                         Comment out titles in tabulated statistics (titleprec)
 
 

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 the web:

   http://bugzilla.bioperl.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/lvb.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob

new

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