Héctor Valverde > Bio-EasyYang > Bio::EasyYang

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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:

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.

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