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Bio::Tools::Phylo::MolUser:Contributed PerBio::Tools::Phylo::Molphy::Result(3)

NAME
       Bio::Tools::Phylo::Molphy::Result - container for data parsed from a
       ProtML run

SYNOPSIS
	 # do not use this object directly, you	will get it back as part of a
	 # Molphy parser
	 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 container for data parsed from	a ProtML run.

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::Result->new();
	Function: Builds a new Bio::Tools::Phylo::Molphy::Result object
	Returns	: Bio::Tools::Phylo::Molphy::Result
	Args	:

   model
	Title	: model
	Usage	: $obj->model($newval)
	Function:
	Returns	: value	of model
	Args	: newvalue (optional)

   substitution_matrix
	Title	: substitution_matrix
	Usage	: my $smat = $result->subsitution_matrix;
	Function: Get the relative substitution	matrix calculated in the ML procedure
	Returns	: reference to hash of hashes where key	is the aa/nt name and value
		  is another hash ref which contains keys for all the aa/nt
		  possibilities
	Args	: none

   transition_probability_matrix
	Title	: transition_probability_matrix
	Usage	: my $matrixref	= $molphy->transition_probablity_matrix();
	Function: Gets the observed transition probability matrix
	Returns	: hash of hashes of aa/nt transition to	each other aa/nt
	Args	: Transition matrix type, typically
		  '1PAM-1.0e05'	or '1PAM-1.0e07'

   residue_frequencies
	Title	: residue_frequencies
	Usage	: my %data = $molphy->residue_frequencies()
	Function: Get the modeled and expected frequencies for
		  each of the residues in the sequence
	Returns	: hash of either aa (protml) or	nt (nucml) frequencies
		  each key will	point to an array reference where
		  1st slot is model's expected frequency
		  2nd slot is observed frequency in the	data
		  $hash{'A'}->[0] =
	Args	: none

   next_tree
	Title	: next_tree
	Usage	: my $tree = $factory->next_tree;
	Function: Get the next tree from the factory
	Returns	: L<Bio::Tree::TreeI>
	Args	: none

   rewind_tree
	Title	: rewind_tree_iterator
	Usage	: $result->rewind_tree()
	Function: Rewinds the tree iterator so that next_tree can be
		  called again from the	beginning
	Returns	: none
	Args	: none

   add_tree
	Title	: add_tree
	Usage	: $result->add_tree($tree);
	Function: Adds a tree
	Returns	: integer which	is the number of trees stored
	Args	: L<Bio::Tree::TreeI>

   search_space
	Title	: search_space
	Usage	: $obj->search_space($newval)
	Function:
	Returns	: value	of search_space
	Args	: newvalue (optional)

perl v5.24.1			  2017-07-Bio::Tools::Phylo::Molphy::Result(3)

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

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