[Bioperl-l] Problem with PAML/Codeml wrapper

Alexander Donath alex at bioinf.uni-leipzig.de
Mon Mar 8 10:45:14 EST 2010


I do have a problem with the PAML/Codeml wrapper. I want to calculate all 
pairwise K_a,K_s values from a given alignment, using the example 
procedure of http://www.bioperl.org/wiki/HOWTO:PAML

     my $dna_aln = aa_to_dna_aln($aln, \%seqs);
     my $kaks_factory = Bio::Tools::Run::Phylo::PAML::Codeml->new(
 	-params => { 'runmode' => -2,
 		     'seqtype' => 1,}

     my ($rc,$parser) = $kaks_factory->run();
     my $result = $parser->next_result();

But I receive an error:

-------------------- WARNING ---------------------
MSG: There was an error - see error_string for the program output

------------- EXCEPTION: Bio::Root::NotImplemented -------------
MSG: Unknown format of PAML output did not see seqtype
STACK: Error::throw
STACK: Bio::Root::Root::throw 
STACK: Bio::Tools::Phylo::PAML::_parse_summary 
STACK: Bio::Tools::Phylo::PAML::next_result 

I use PAML4.4. Could this be the reason?


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