NAME

Bio::Tools::Run::PiseApplication::quicktree

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::quicktree

      Bioperl class for:

        QuickTree       Rapid reconstruction of phylogenies by the Neighbor-Joining method (Kevin Howe, Alex Bateman, Richard Durbin)

        References:

                Kevin Howe, Alex Bateman and Richard Durbin  (2002). QuickTree: building huge Neighbour-Joining trees of protein sequences. Bioinformatics 18(11):1546-1547.



      Parameters: 

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


                quicktree (String)

                distfile (InFile)
                        Distance matrix (-in m)
                        pipe: phylip_dist

                out (Excl)
                        Output (-out)

                upgma (Switch)
                        Use the UPGMA method to construct the tree (-upgma)

                aligfile (InFile)
                        Protein alignment file (instead of distance matrix) (-in a)
                        pipe: readseq_ok_alig

                boot (Integer)
                        Calculate bootstrap values with n iterations (-boot)

                kimura (Switch)
                        Use the kimura translation for pairwise distances (-kimura)

                fastdnaml (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/quicktree.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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