NAME

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

SYNOPSIS

         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
         }

DESCRIPTION

       A parser for Molphy output (protml,dnaml)

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

       Email jason-at-bioperl.org

APPENDIX

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

   new
        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

   next_result
        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