NAME

Bio::Tools::Run::PiseApplication::distquart

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::distquart

      Bioperl class for:

        PHYLOQUART      distquart - quartet inference by weak four-point method (NJ) (Berry)


      Parameters: 

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


                distquart (String)

                dist (Switch)
                        Reads as input inter-species distances (as opposed to sequences) (-d)

                infile (Sequence)
                        Nucleotide Sequences Alignement File
                        pipe: readseq_ok_alig

                gap (Switch)
                        Use gap position whenever is possible for computing the distance between two taxa (-g)

                correct (Excl)
                        Evolutionary model correction (-c)

                savedist (Switch)
                        Save in the file outfile.dist the inter-species Hamming distances computed from the input nucleotide sequences (-s)

                distfile (InFile)
                        Distances matrix File (lower triangular)
                        pipe: phylip_dist

                lower (Switch)
                        Lower triangular distances matrix (-l)

                outdistfile (OutFile)
                        pipe: phylip_dist

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/distquart.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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