Bio::Tools::Phylo::Molphy(3pm)				User Contributed Perl Documentation			    Bio::Tools::Phylo::Molphy(3pm)

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, "
";

	   # 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
",
		 $smat->{'Arg'}->{'Gln'}, "
";

	   # 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
",
		 $tmat->{'Arg'}->{'Gln'}, "
";

	   # 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
",
		     $residue,$rfreqs->{$residue}->[0], $rfreqs->{$residue}->[1];
	   }

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

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

	   # 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://redmine.open-bio.org/projects/bioperl/

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

perl v5.14.2							    2012-03-02					    Bio::Tools::Phylo::Molphy(3pm)