Bio::Tools::Run::PiseApplication::Puzzle(3)

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.