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.