NAME

Bio::Tools::Run::PiseApplication::clique

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::clique

      Bioperl class for:

	Phylip	clique - Compatibility Program (Felsenstein)

	References:

		Felsenstein, J.  1993.  PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author.  Department of Genetics, University of Washington, Seattle.

		Felsenstein, J.  1989.  PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics  5: 164-166.



      Parameters: 

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


		clique (String)

		infile (InFile)
			Input File

		use_ancestral_state (Switch)
			Use ancestral states in input file (A)

		spec_min_clique_size (Switch)
			Specify minimum clique size? (C)

		min_clique_size (Integer)
			Minimum clique size

		multiple_dataset (Switch)
			Analyze multiple data sets (M)

		datasets_nb (Integer)
			How many data sets

		consense (Switch)
			Compute a consensus tree

		print_matrix (Switch)
			Print out compatibility matrix (3)

		print_tree (Switch)
			Print out tree (4)

		print_treefile (Switch)
			Write out trees onto tree file (5)

		printdata (Switch)
			Print out the data at start of run (1)

		indent_tree (Switch)
			Indent treefile

		outgroup (Integer)
			Outgroup root (default, use as outgroup species 1) (O)

		confirm (String)

		terminal_type (String)

		consense_confirm (String)

		consense_terminal_type (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/clique.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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