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>
<hvalverde at uma.es>
Juan Carlos Aledo, <caledo@uma.es>
<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.
bug-bio-easyyang at rt.cpan.org
You can find documentation for this module with the perldoc command.
perldoc Bio::EasyYang
You can also look for information at:
RT: CPAN's request tracker (report bugs here)
http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-EasyYang
AnnoCPAN: Annotated CPAN documentation
http://annocpan.org/dist/Bio-EasyYang
CPAN Ratings
http://cpanratings.perl.org/d/Bio-EasyYang
Search CPAN
http://search.cpan.org/dist/Bio-EasyYang/
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.
To install Bio::EasyYang, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::EasyYang
CPAN shell
perl -MCPAN -e shell install Bio::EasyYang
For more information on module installation, please visit the detailed CPAN module installation guide.