NAME

Bio::Tools::Run::PiseApplication::prot_nucml

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::prot_nucml

      Bioperl class for:

        Molphy  ProtML, NucML phylogeny programs (J. Adachi & M. Hasegawa)


      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/prot_nucml.html 
         for available values):


                prot_nucml (Excl)
                        Program

                interleaved (String)

                tee (String)

                results (OutFile)
                        pipe: phylip_dist

                outtree (OutFile)
                        pipe: phylip_tree

                sequences (Sequence)
                        Sequences File (protml or nucml)
                        pipe: readseq_ok_alig

                modelprot (Excl)
                        Model for ProtML

                modeldna (Excl)
                        Model for NucML

                n1 (Integer)
                        n1 : Alpha/Beta ratio (default:4.0) (option : -t n1)

                n2 (Integer)
                        n2 AlphaY/AlphaR ratio (default:1.0) (option : -t n1,n2)

                mode (Excl)
                        Strategy or Mode

                topology (InFile)
                        Topology File (if Users Tree mode or Exhaustive       search or local Rearrangement search)

                num (Integer)
                        Retained top ranking trees (-n)

                verbose (Switch)
                        Verbose to stderr (-v)

                info (Switch)
                        Output some informations (-i -w)

                boot (Switch)
                        no Bootstrap probabilities (Users trees) (-b)

                minimum_evolution (Switch)
                        Minimum evolution (with -e) (-M)

                sequential (Switch)
                        Sequential format (-S)

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/prot_nucml.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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