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Christopher Fields
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Bio::Tools::Phylo::PAML - Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00


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

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

  # 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 = Bio::Tools::Phylo::PAML->new
    (-file => "./results/mlc", -dir => "./results/");

  # get the first/next result; a Bio::Tools::Phylo::PAML::Result object,
  # which isa Bio::SeqAnalysisResultI 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" and "kappa" will also be defined.
  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_trees();
  for my $node ($tree->get_nodes()) {
     # inspect the tree: the "t" (time) parameter is available via
     # $node->branch_length(); all other branch-specific parameters
     # ("omega", "dN", etc.) are available via 
     # ($omega) = $node->get_tag_values('omega');

  # if you are using model based Codeml then trees are stored in each 
  # modelresult object
  for my $modelresult ( $result->get_NSSite_results ) {
    # model M0, M1, etc
    print "model is ", $modelresult->model_num, "\n";
    my ($tree) = $modelresult->get_trees();
    for my $node ($tree->get_nodes()) {
     # inspect the tree: the "t" (time) parameter is available via
     # $node->branch_length(); all other branch-specific parameters
     # ("omega", "dN", etc.) are available via 
     # ($omega) = $node->get_tag_values('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};

  # parse AAML result files
  my $aamat = $result->get_AADistMatrix();
  my $aaMLmat = $result->get_AAMLDistMatrix();


This module is used to parse the output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio::Tools::Run::Phylo::PAML::* modules to actually run some of the PAML programs, but this module is only useful to parse the output.


Implement get_posteriors(). For NSsites models, obtain arrayrefs of 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"; }


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AUTHOR - Jason Stajich, Aaron Mackey

Email jason-at-bioperl.org Email amackey-at-virginia.edu


Albert Vilella avilella-AT-gmail-DOT-com Sendu Bala bix@sendu.me.uk


RST parsing -- done, Avilella contributions bugzilla#1506, added by jason 1.29 -- still need to parse in joint probability and non-syn changes at site table


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


 Title   : new
 Usage   : my $obj = Bio::Tools::Phylo::PAML->new(%args);
 Function: Builds a new Bio::Tools::Phylo::PAML object
 Returns : Bio::Tools::Phylo::PAML
 Args    : Hash of options: -file, -fh, -dir
           -file (or -fh) should contain the contents of the PAML
           -dir is the (optional) name of the directory in
                which the PAML program was run (and includes other
                PAML-generated files from which we can try to gather data)

Implement Bio::AnalysisParserI interface


 Title   : next_result
 Usage   : $result = $obj->next_result();
 Function: Returns the next result available from the input, or
           undef if there are no more results.
 Example :
 Returns : a Bio::Tools::Phylo::PAML::Result object
 Args    : none