Bio::EasyYang - A tiny interface for Bio::Tools::Run::Phylo::PAML::Yn00 module
Version 1.00
use Bio::AlignIO;
use Bio::EasyYang;
my $alnio = Bio::AlignIO(-file => 'align.fas', -format => 'fasta');
my $aln = $alnio->next_aln;
my $genetic_code = 1; # Id for vertebrate mitochondrial
my %result = Bio::EasyYang->yang($aln,$genetic_code);
foreach my $key (keys %result){
print "$key = $result{$key}\n";
}
This module is a simple function to execute the Yang algorithm easily.
This function returns the results from Yang's calcs:
Title : yang
Usage : Bio::EasyYang->yang($alignment,$genetic_code)
Function: Runs the Yang Algorithm easily
Returns : A hash with the results:
%hash = (
yang_table => $out_str,
N => \@N,
S => \@S,
dN => \@dN,
dS => \@dS,
dN_VAR => \@dN_VAR,
dS_VAR => \@dS_VAR,
omega => \@omega,
kappa => \@kappa,
t => \@t
);
Args : $alignment -> A Bio::SimpleAlignm object,
$genetic_code -> Integer, the number corresponding to the
genetic code (see L<<Bio::Tools::Run::Phylo::PAML::Yn00>>
for avaliable genetic codes).
Hector Valverde, <hvalverde at uma.es>
Juan Carlos Aledo, <caledo@uma.es>
Please report any bugs or feature requests to bug-bio-easyyang at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-EasyYang. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.
You can find documentation for this module with the perldoc command.
perldoc Bio::EasyYang
You can also look for information at:
Copyright 2012 Hector Valverde.
This program is free software; you can redistribute it and/or modify it under the terms of either: the GNU General Public License as published by the Free Software Foundation; or the Artistic License.
See http://dev.perl.org/licenses/ for more information.
