NAME

Bio::Tools::Run::PiseApplication::filtersites

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::filtersites

      Bioperl class for:

        filtersites     Filter conserved sites in an alignment (K. Schuerer)


      Parameters: 

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


                filtersites (String)

                outalig (OutFile)
                        pipe: readseq_ok_alig

                outweights (OutFile)
                        pipe: phylip_weights

                infile (Sequence)
                        Alignment
                        pipe: readseq_ok_alig

                threshold (Float)
                        Threshold (-t)

                weights (Switch)
                        Phylip weights file rather than filtered alignment (for parsimony programs only) (-w)

                phylip_alig (Switch)
                        Phylip alignment output format

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/filtersites.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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