Bio::Tools::Run::PiseApplication::Puzzle # 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.