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