NAME

Bio::EasyYang - A tiny interface for Bio::Tools::Run::Phylo::PAML::Yn00 module

VERSION

Version 1.00

SYNOPSIS

            

              
              
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";
}
            
          

DESCRIPTION

This module is a simple function to execute the Yang algorithm easily.

FUNCTIONS

yang

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).
            
          

AUTHOR

Hector Valverde, <hvalverde at uma.es>

CONTRIBUTORS

Juan Carlos Aledo, <caledo@uma.es>

BUGS

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.

SUPPORT

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/

LICENSE AND COPYRIGHT

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.