NAME

Bio::Tools::Run::PiseApplication::Puzzle

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::Puzzle

      Bioperl class for:

	Puzzle	Tree reconstruction for sequences by quartet puzzling and maximum likelihood (Strimmer, von Haeseler)

	References:

		Strimmer, K., and A. von Haeseler. 1996. Quartet puzzling:A quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13: 964-969.



      Parameters: 

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


		Puzzle (String)

		stdinput (String)

		confirm (String)

		infile (Sequence)
			Alignement File
			pipe: readseq_ok_alig

		seqtype (Excl)
			Is it a DNA or protein sequence

		approximate (Switch)
			Approximate quartet likelihood (v)

		puzzling_step (Integer)
			Number of puzzling steps (n)

		protein_model (Excl)
			Model of substitution for protein (if no automatic guess) (m)

		ratio (Float)
			Transition/transversion ratio (t)

		GTR_acrate (Float)
			A-C rate (1)

		GTR_agrate (Float)
			A-G rate (2)

		GTR_atrate (Float)
			A-T rate (3)

		GTR_cgrate (Float)
			C-G rate (4)

		GTR_ctrate (Float)
			C-T rate (5)

		GTR_gtrate (Float)
			G-T rate (6)

		use_specified (Switch)
			Use specified values

		a_freq (Float)
			pi(A)

		c_freq (Float)
			pi(C)

		g_freq (Float)
			pi(G)

		dna_model (Excl)
			Model of substitution for DNA (m)

		constrain_TN (Switch)
			Constrain TN model to F84 model (p)

		f84_ratio (Float)
			Expected F84 Transition/transversion ratio

		y_r (Float)
			Y/R transition parameter (r)

		symmetrize_frequencies (Switch)
			Symmetrize doublet frequencies (s)

		rate_heterogeneity (Excl)
			Model of rate heterogeneity (w)

		alpha (Float)
			Gamma distribution parameter alpha (a)

		gamma_number (Integer)
			Number of Gamma rate categories (c)

		invariable (Float)
			Fraction of invariable sites (i)

		user_tree (Switch)
			Tree search procedure: User tree (k)

		tree_file (InFile)
			User Tree file

		no_tree (Switch)
			Pairwise distances only (no tree) (k)

		outgroup (Integer)
			Display as outgroup (o)

		branch_length (Switch)
			Compute clocklike branch lengths (z)

		estimates (Excl)
			Parameter estimates (e)

		estimation_by (Excl)
			Parameter estimation by (x)

		list_unresolved (Switch)
			List unresolved quartets (u)

		list_trees (Switch)
			List puzzling step trees (j)

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/Puzzle.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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