Bio::Tools::Run::PiseApplication::Puzzle.3pm

Langue: en

Autres versions - même langue

Version: 2002-11-20 (mandriva - 01/05/08)

Section: 3 (Bibliothèques de fonctions)

Sommaire

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.