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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

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/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.