Bio::Tools::Run::PiseApplication::Puzzle
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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:
(see also:
http://bioweb.pasteur.fr/seqanal/interfaces/Puzzle.html
for available values):
Puzzle (String)
stdinput (String)
confirm (String)
infile (Sequence)
Alignement File
pipe: readseq_ok_alig
seqtype (Excl)
Is it a DNA or protein sequence
approximate (Switch)
Approximate quartet likelihood (v)
puzzling_step (Integer)
Number of puzzling steps (n)
protein_model (Excl)
Model of substitution for protein (if no automatic guess) (m)
ratio (Float)
Transition/transversion ratio (t)
GTR_acrate (Float)
A-C rate (1)
GTR_agrate (Float)
A-G rate (2)
GTR_atrate (Float)
A-T rate (3)
GTR_cgrate (Float)
C-G rate (4)
GTR_ctrate (Float)
C-T rate (5)
GTR_gtrate (Float)
G-T rate (6)
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_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 (Switch)
Tree search procedure: User tree (k)
tree_file (InFile)
User Tree file
no_tree (Switch)
Pairwise distances only (no tree) (k)
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)
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
http://bugzilla.open-bio.org/
Catherine Letondal (letondal@pasteur.fr)
Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.
This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
This software is provided "as is" without warranty of any kind.
Title : new() Usage : my $Puzzle = Bio::Tools::Run::PiseApplication::Puzzle->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::Puzzle object. This method should not be used directly, but rather by a Bio::Tools::Run::AnalysisFactory::Pise instance. my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new(); my $Puzzle = $factory->program('Puzzle'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::Puzzle.
