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Bio::Tools::Phylo::MolUser3Contributed Perl DocumeBio::Tools::Phylo::Molphy(3)

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

perl v5.32.1			  2019-12-07	  Bio::Tools::Phylo::Molphy(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

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