NAME

Bio::Tools::Run::PiseApplication::pars

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::pars

      Bioperl class for:

	Phylip	pars - Discrete character parsimony (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/pars.html 
         for available values):


		pars (String)

		infile (InFile)
			Input File

		search_opt (Excl)
			Search option (S)

		save_trees (Integer)
			 Number of trees to save? (V)

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

		jumble (Switch)
			Randomize (jumble) input order (J)

		jumble_seed (Integer)
			Random number seed (must be odd)

		times (Integer)
			Number of times to jumble

		weights (Switch)
			Weighted sites (W)

		weight_file (InFile)
			Weight file

		user_tree (Switch)
			Use User tree (default: no, search for best tree) (U)

		tree_file (InFile)
			User Tree file

		tree_nb (Integer)
			How many tree(s) in the User Tree file

		multiple_dataset (Switch)
			Analyze multiple data sets (M)

		datasets_nb (Integer)
			How many data sets

		consense (Switch)
			Compute a consensus tree

		print_tree (Switch)
			Print out tree (3)

		print_step (Switch)
			Print out steps in each character (4)

		print_states (Switch)
			Print states at all nodes of tree (5)

		print_treefile (Switch)
			Write out trees onto tree file (6)

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

		indent_tree (Switch)
			Indent treefile

		use_threshold (Switch)
			Use Threshold parsimony (T)

		threshold (Integer)
			Threshold value (if use threshold parsimony)

		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/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/pars.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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