[Bioperl-l] PAML Codeml version supported

[Frantz, Laurent]

Dear Bioperl Gurus,

I have a large set of genes that I need to check separately for dS/dN. I am trying to use the Bioperl wrapper for PAML, however I can not get it to work.
I have read that there are problems with the output of newer version of PAML that does not fit to the wrapper. I have tried 4.4, 4.1 and then 3.15 none of those work.

Here is my error message (same with all those versions):

------------- EXCEPTION: Bio::Root::NotImplemented -------------
MSG: Unknown format of PAML output did not see seqtype
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
STACK: Bio::Tools::Phylo::PAML::_parse_summary /usr/local/share/perl/5.10.1/Bio/Tools/Phylo/PAML.pm:461
STACK: Bio::Tools::Phylo::PAML::next_result /usr/local/share/perl/5.10.1/Bio/Tools/Phylo/PAML.pm:270
STACK: paml_gene_parse.pl:26
----------------------------------------------------------------

Could anyone tell me which of the PAML - Codeml versions gives an output that can be parsed by Bioperl?
I am surprised that it does not work with the version 3.15 as it is suppose to (http://www.bioperl.org/wiki/PAML). 

I am also wondering if my syntax is correct.

@files = @ARGV;

foreach $files (@files) {
        my $kaks_factory = Bio::Tools::Run::Phylo::PAML::Codeml->new
        ( -params => { 'runmode' => -2,
                        'seqtype' => 1,
                                   } );
        $kaks_factory->alignment($files);
        my ($rc,$parser) = $kaks_factory->run();
        my $result = $parser->next_result;
        my $MLmatrix = $result->get_MLmatrix();
        print "$MLmatrix\n";
}

The files that I input are already formated for Codeml, they work perfectly fine when I feed them myself to Codeml through the config file.

I hope someone can help me..
Thank you,

Laurent Frantz
PhD Student - Comparative Genomics
Wageningen University
laurent.frantz at wur.nl