Provided by: libbio-perl-perl_1.7.6-3_all bug


       Bio::Tools::Phylo::Molphy - parser for Molphy output


         use Bio::Tools::Phylo::Molphy;
         my $parser = Bio::Tools::Phylo::Molphy->new(-file => 'output.protml');
         while( my $r = $parser->next_result ) {
           # r is a Bio::Tools::Phylo::Molphy::Result object

           # print the model name
           print $r->model, "\n";

           # get the substitution matrix
           # this is a hash of 3letter aa codes -> 3letter aa codes representing
           # substitution rate
           my $smat = $r->substitution_matrix;
           print "Arg -> Gln substitution rate is %d\n",
                 $smat->{'Arg'}->{'Gln'}, "\n";

           # get the transition probablity matrix
           # this is a hash of 3letter aa codes -> 3letter aa codes representing
           # transition probabilty
           my $tmat = $r->transition_probability_matrix;
           print "Arg -> Gln transition probablity is %.2f\n",
                 $tmat->{'Arg'}->{'Gln'}, "\n";

           # get the frequency for each of the residues
           my $rfreqs = $r->residue_frequencies;

           foreach my $residue ( keys %{$rfreqs} ) {
              printf "residue %s  expected freq: %.2f observed freq: %.2f\n",
                     $residue,$rfreqs->{$residue}->[0], $rfreqs->{$residue}->[1];

           my @trees;
           while( my $t = $r->next_tree ) {
               push @trees, $t;

           print "search space is ", $r->search_space, "\n",
                 "1st tree score is ", $trees[0]->score, "\n";

           # writing to STDOUT, use -file => '>filename' to specify a file
           my $out = Bio::TreeIO->new(-format => "newick");
           $out->write_tree($trees[0]); # writing only the 1st tree


       A parser for Molphy output (protml,dnaml)


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AUTHOR - Jason Stajich



       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::Molphy->new();
        Function: Builds a new Bio::Tools::Phylo::Molphy object
        Returns : Bio::Tools::Phylo::Molphy
        Args    : -fh/-file => $val, # for initing input, see Bio::Root::IO

        Title   : next_result
        Usage   : my $r = $molphy->next_result
        Function: Get the next result set from parser data
        Returns : Bio::Tools::Phylo::Molphy::Result object
        Args    : none