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