BioPerl Mailing List Summaries

The first of a biweekly summary of BioPerl mailing list summaries has been posted to the wiki:

These will likely be archived on the wiki but may be moved to a more suitable location in the future (maybe to this blog?).

2 thoughts on “BioPerl Mailing List Summaries”

  1. todaewon says:

    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’,

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

    my $yn = new Bio::Tools::Run::Phylo::PAML::Yn00();
    my ($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 = $kaksn”;

  2. Chris Fields says:

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

    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.

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