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:


		Puzzle (String)

		stdinput (String)

		confirm (String)

		outfile (Results)

		outtree (Results)
			pipe: phylip_tree

		outdist (Results)
			pipe: phylip_dist

		params (Results)

		infile (Sequence)
			Alignement File
			pipe: readseq_ok_alig

		seqtype (Excl)
			Is it a DNA or protein sequence

		control_options (Paragraph)
			Control options

		approximate (Switch)
			Approximate quartet likelihood (v)

		puzzling_step (Integer)
			Number of puzzling steps (n)

		protein_options (Paragraph)
			Protein options

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

		dna_options (Paragraph)
			DNA options

		ratio (Float)
			Transition/transversion ratio (t)

		nuc_freq (Paragraph)
			Nucleotids frequencies (in %) (f)

		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_options (Paragraph)
			Rate heterogeneity options

		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_options (Paragraph)
			User Tree options

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

		tree_file (InFile)
			User Tree file

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

		output_options (Paragraph)
			Output options

		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)

new

Title   : new()
Usage   : my $Puzzle = Bio::Tools::Run::PiseApplication::Puzzle->new($remote, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::Puzzle object.
          This method should not be used directly, but rather by 
          a Bio::Factory::Pise instance:
          my $factory = Bio::Factory::Pise->new(-email => 'me@myhome');
          my $Puzzle = $factory->program('Puzzle');
Example :
Returns : An instance of Bio::Tools::Run::PiseApplication::Puzzle.