Provided by: libbio-perl-perl_1.6.901-2_all bug


       Bio::Tools::Phylo::PAML::Codeml - Parses output from the PAML program codeml.


         #!/usr/bin/perl -Tw
         use strict;

         use Bio::Tools::Phylo::PAML::Codeml;

         # need to specify the output file name (or a fh) (defaults to
         # -file => "codeml.mlc"); also, optionally, the directory in which
         # the other result files (rst, 2ML.dS, etc) may be found (defaults
         # to "./")
         my $parser = new Bio::Tools::Phylo::PAML::Codeml::Parser
           (-file => "./results/mlc", -dir => "./results/");

         # get the first/next result; a Bio::[...]::Codeml::Result object
         my $result = $parser->next_result();

         # get the sequences used in the analysis; returns Bio::PrimarySeq
         # objects (OTU = Operational Taxonomic Unit).
         my @otus = $result->get_seqs();

         # codon summary: codon usage of each sequence [ arrayref of {
         # hashref of counts for each codon } for each sequence and the
         # overall sum ], and positional nucleotide distribution [ arrayref
         # of { hashref of frequencies for each nucleotide } for each
         # sequence and overall frequencies ].

         my ($codonusage, $ntdist) = $result->get_codon_summary();

         # example manipulations of $codonusage and $ntdist:
         printf "There were %d '%s' codons in the first seq (%s)\n",
           $codonusage->[0]->{AAA}, 'AAA', $otus[0]->id();
         printf "There were %d '%s' codons used in all the sequences\n",
           $codonusage->[$#{$codonusage}]->{AAA}, 'AAA';
         printf "Nucleotide '%c' was present %g of the time in seq %s\n",
           'A', $ntdist->[1]->{A}, $otus[1]->id();

         # get Nei & Gojobori dN/dS matrix:
         my $NGmatrix = $result->get_NGmatrix();

         # get ML-estimated dN/dS matrix, if calculated; this corresponds to
         # the runmode = -2, pairwise comparison usage of codeml
         my $MLmatrix = $result->get_MLmatrix();

         # These matrices are length(@otu) x length(@otu) "strict lower
         # triangle" 2D-matrices, which means that the diagonal and
         # everything above it is undefined.  Each of the defined cells is a
         # hashref of estimates for "dN", "dS", "omega" (dN/dS ratio), "t",
         # "S" and "N".  If a ML matrix, "lnL" will also be defined.  Any
         # additional ML parameters estimated by the model will be in an
         # array ref under "params"; it's up to the user to know which
         # position corresponds to which parameter (since PAML doesn't label
         # them, and we can't guess very well yet (a TODO I guess).

         printf "The omega ratio for sequences %s vs %s was: %g\n",
           $otus[0]->id, $otus[1]->id, $MLmatrix->[0]->[1]->{omega};

         # with a little work, these matrices could also be passed to
         # Bio::Tools::Run::Phylip::Neighbor, or other similar tree-building
         # method that accepts a matrix of "distances" (using the LOWTRI
         # option):
         my $distmat = [ map { [ map { $$_{omega} } @$_ ] } @$MLmatrix ];

         # for runmode's other than -2, get tree topology with estimated
         # branch lengths; returns a Bio::Tree::TreeI-based tree object with
         # added PAML parameters at each node
         my $tree = $result->get_tree();
         for my $node ($tree->get_nodes()) {
            # inspect the tree: the "t" (time) parameter is available via
            # $node->branch_length(); all other branch-specific parameters
            # ("omega", "dN", etc.) are available via $node->param('omega');

         # get any general model parameters: kappa (the
         # transition/transversion ratio), NSsites model parameters ("p0",
         # "p1", "w0", "w1", etc.), etc.
         my $params = $result->get_model_params();
         printf "M1 params: p0 = %g\tp1 = %g\n", $params->{p0}, $params->{p1};

         # for NSsites models, obtain posterior probabilities for membership
         # in each class for every position; probabilities correspond to
         # classes w0, w1, ... etc.
         my @probs = $result->get_posteriors();

         # find, say, positively selected sites!
         if ($params->{w2} > 1) {
           for (my $i = 0; $i < @probs ; $i++) {
             if ($probs[$i]->[2] > 0.5) {
                # assumes model M1: three w's, w0, w1 and w2 (positive selection)
                printf "position %d: (%g prob, %g omega, %g mean w)\n",
                  $i, $probs[$i]->[2], $params->{w2}, $probs[$i]->[3];
         } else { print "No positive selection found!\n"; }


       This module is used to parse the output from the PAML program codeml.  You can use the
       Bio::Tools::Run::Phylo::Phylo::PAML::Codeml module to actually run codeml; this module is
       only useful to parse the output.


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AUTHOR - Jason Stajich, Aaron Mackey

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       This module should also be able to handle "codemlsites" batch output...


       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

        Title   : new
        Usage   : my $obj = new Bio::Tools::Phylo::PAML::Codeml();
        Function: Builds a new Bio::Tools::Phylo::PAML::Codeml object
        Returns : Bio::Tools::Phylo::PAML::Codeml
        Args    :

        Title   : get_trees
        Usage   : my @trees = $codemlparser->get_trees();
        Function: Returns a list of trees (if any) are in the output file
        Returns : List of L<Bio::Tree::TreeI> objects
        Args    : none

        Title   : get_statistics
        Usage   : my $data = $codemlparser->get_statistics
        Function: Retrieves the set of pairwise comparisons
        Returns : Hash Reference keyed as 'seqname' -> 'seqname' -> 'datatype'
        Args    : none