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1. 2 Responses to “BioPerl Mailing List Summaries”

2. I just coded according to howto manual
   but I can’t get any result. there is no error message~!~

   what’s happen??

   use lib “/usr/local/lib/perl5/site_perl/5.8.7″;
   use Bio::Tools::Run::Phylo::PAML::Yn00;
   use Bio::AlignIO;
   my $alignio = new Bio::AlignIO(-format => ‘phylip’,
   -file => ‘/r1/people/daewon_kim/ Oranutan_cDNA/2.Processing/4.CodonC/dNdSGene1.phylip’,

   -idlength=>12,
   -interleaved => 1);
   my $aln = $alignio->next_aln;

   my $yn = new Bio::Tools::Run::Phylo::PAML::Yn00();
   $yn->alignment($aln);
   my ($rc,$parser) = $yn->run();

   if(my $result = $parser->next_result) {
   my @otus = $result->get_seqs();
   my $MLmatrix = $result->get_MLmatrix();
   # 0 and 1 correspond to the 1st and 2nd entry in the @otus array
   my $dN = $MLmatrix->[0]->[1]->{dN};
   my $dS = $MLmatrix->[0]->[1]->{dS};
   my $kaks =$MLmatrix->[0]->[1]->{omega};
   print “Ka = $dN Ks = $dS Ka/Ks = $kaks\n”;
   }

   By todaewon on Jun 24, 2006

3. You should be posting this to the mail list and not here:

   http://bioperl.org/mailman/listinfo/bioperl-l

   BTW, Bio::Tools::Run::Phylo::PAML::Yn00/codeml were recently updated to deal with results from PAML 3.15 which could be your problem, but you’ll have to update from CVS.

   By Chris Fields on Jun 24, 2006

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