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Bio::Tools::Phylo::PAMUseroContributed)Bio::Tools::Phylo::PAML::ModelResult(3)

NAME
       Bio::Tools::Phylo::PAML::ModelResult - A	container for NSSite Model
       Result from PAML

SYNOPSIS
	 # get a ModelResult from a PAML::Result object
	 use Bio::Tools::Phylo::PAML;
	 my $paml = Bio::Tools::Phylo::PAML->new(-file => 'mlc');
	 my $result = $paml->next_result;
	 foreach my $model ( $result->get_NSSite_results ) {
	   print $model->model_num, " ", $model->model_description, "\n";
	   print $model->kappa,	"\n";
	   print $model->run_time, "\n";
       # if you	are using PAML < 3.15 then only	one place for POS sites
	  for my $sites	( $model->get_pos_selected_sites ) {
	   print join("\t",@$sites),"\n";
	  }
       # otherwise query NEB and BEB slots
	  for my $sites	( $model->get_NEB_pos_selected_sites ) {
	    print join("\t",@$sites),"\n";
	  }

	  for my $sites	( $model->get_BEB_pos_selected_sites ) {
	   print join("\t",@$sites),"\n";
	  }

	 }

DESCRIPTION
       Describe	the object here

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 email
       or the web:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich
       Email jason@open-bio.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::PAML::ModelResult->new();
	Function: Builds  a new	Bio::Tools::Phylo::PAML::ModelResult object
	Returns	: an instance of Bio::Tools::Phylo::PAML::ModelResult
	Args	: -model_num	       => model	number
		  -model_description   => model	description
		  -kappa	       => value	of kappa
		  -time_used	       => amount of time
		  -pos_sites	       => arrayref of sites under positive selection
		  -neb_sites	       => arrayref of sites under positive selection (by NEB analysis)
		  -beb_sites	       => arrayref of sites under positive selection (by BEB analysis)
		  -trees	       => arrayref of tree(s) data for this model
		  -shape_params	       => hashref of parameters
					  ('shape' => 'alpha',
					   'gamma' => $g,
					   'r' => $r,
					   'f' => $f
					   )
					   OR
					   ( 'shape' =>	'beta',
					     'p' => $p,
					     'q' => $q
					    )
		  -likelihood	       => likelihood
		  -num_site_classes    => number of site classes
		  -dnds_site_classes   => hashref with two keys, 'p' and 'w'
					  which	each point to an array,	each
					  slot is for a	different site class.
					  'w' is for dN/dS and 'p' is probability

   model_num
	Title	: model_num
	Usage	: $obj->model_num($newval)
	Function: Get/Set the Model number (0,1,2,3...)
	Returns	: value	of model_num (a	scalar)
	Args	: on set, new value (a scalar or undef,	optional)

   model_description
	Title	: model_description
	Usage	: $obj->model_description($newval)
	Function: Get/Set the model description
		  This is something like 'one-ratio', 'neutral', 'selection'
	Returns	: value	of description (a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

   time_used
	Title	: time_used
	Usage	: $obj->time_used($newval)
	Function: Get/Set the time it took to run this analysis
	Returns	: value	of time_used (a	scalar)
	Args	: on set, new value (a scalar or undef,	optional)

   kappa
	Title	: kappa
	Usage	: $obj->kappa($newval)
	Function: Get/Set kappa	(ts/tv)
	Returns	: value	of kappa (a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

   num_site_classes
	Title	: num_site_classes
	Usage	: $obj->num_site_classes($newval)
	Function: Get/Set the number of	site classes for this model
	Returns	: value	of num_site_classes (a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

   dnds_site_classes
	Title	: dnds_site_classes
	Usage	: $obj->dnds_site_classes($newval)
	Function: Get/Set dN/dS	site classes, a	hashref
		  with 2 keys, 'p' and 'w' which point to arrays
		  one slot for each site class.
	Returns	: value	of dnds_site_classes (a	hashref)
	Args	: on set, new value (a scalar or undef,	optional)

   get_pos_selected_sites
	Title	: get_pos_selected_sites
	Usage	: my @sites = $modelresult->get_pos_selected_sites();
	Function: Get the sites	which PAML has identified as under positive
		  selection (w > 1).  This returns an array with each slot
		  being	a site,	4 values,
		  site location	(in the	original alignment)
		  Amino	acid	(I *think* in the first	sequence)
		  P		(P value)
		  Significance	(** indicated >	99%, * indicates >=95%)
	Returns	: Array
	Args	: none

   add_pos_selected_site
	Title	: add_pos_selected_site
	Usage	: $result->add_pos_selected_site($site,$aa,$pvalue,$signif);
	Function: Add a	site to	the list of positively selected	sites
	Returns	: count	of the number of sites stored
	Args	: $site	  - site number	(in the	alignment)
		  $aa	  - amino acid under selection
		  $pvalue - float from 0->1 represent probability site is under	selection according to this model
		  $signif - significance (coded	as either empty, '*', or '**'

   get_NEB_pos_selected_sites
	Title	: get_NEB_pos_selected_sites
	Usage	: my @sites = $modelresult->get_NEB_pos_selected_sites();
	Function: Get the sites	which PAML has identified as under positive
		  selection (w > 1) using Naive	Empirical Bayes.
		  This returns an array	with each slot being a site, 4 values,
		  site location	(in the	original alignment)
		  Amino	acid	(I *think* in the first	sequence)
		  P		(P value)
		  Significance	(** indicated >	99%, * indicates > 95%)
		  post mean for	w
	Returns	: Array
	Args	: none

   add_NEB_pos_selected_site
	Title	: add_NEB_pos_selected_site
	Usage	: $result->add_NEB_pos_selected_site($site,$aa,$pvalue,$signif);
	Function: Add a	site to	the list of positively selected	sites
	Returns	: count	of the number of sites stored
	Args	: $site	  - site number	(in the	alignment)
		  $aa	  - amino acid under selection
		  $pvalue - float from 0->1 represent probability site is under	selection according to this model
		  $signif - significance (coded	as either empty, '*', or '**'
		  $postmean - post mean	for w

   get_BEB_pos_selected_sites
	Title	: get_BEB_pos_selected_sites
	Usage	: my @sites = $modelresult->get_BEB_pos_selected_sites();
	Function: Get the sites	which PAML has identified as under positive
		  selection (w > 1) using Bayes	Empirical Bayes.
		  This returns an array	with each slot being a site, 6 values,
		  site location	(in the	original alignment)
		  Amino	acid	(I *think* in the first	sequence)
		  P		(P value)
		  Significance	(** indicated >	99%, * indicates > 95%)
		  post mean for	w (mean)
		  Standard Error for w (SE)
	Returns	: Array
	Args	: none

   add_BEB_pos_selected_site
	Title	: add_BEB_pos_selected_site
	Usage	: $result->add_BEB_pos_selected_site($site,$aa,$pvalue,$signif);
	Function: Add a	site to	the list of positively selected	sites
	Returns	: count	of the number of sites stored
	Args	: $site	  - site number	(in the	alignment)
		  $aa	  - amino acid under selection
		  $pvalue - float from 0->1 represent probability site is under	selection according to this model
		  $signif - significance (coded	as either empty, '*', or '**'
		  $postmean - post mean	for w
		  $SE	    - Standard Error for w

   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

   get_trees
	Title	: get_trees
	Usage	: my @trees = $result->get_trees;
	Function: Get all the parsed trees as an array
	Returns	: Array	of trees
	Args	: none

   rewind_tree_iterator
	Title	: rewind_tree_iterator
	Usage	: $result->rewind_tree_iterator()
	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>

   shape_params
	Title	: shape_params
	Usage	: $obj->shape_params($newval)
	Function: Get/Set shape	params for the distribution, 'alpha', 'beta'
		  which	is a hashref
		  with 1 keys, 'p' and 'q'
	Returns	: value	of shape_params	(a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

   likelihood
	Title	: likelihood
	Usage	: $obj->likelihood($newval)
	Function: log likelihood
	Returns	: value	of likelihood (a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

perl v5.24.1			  2017-Bio::Tools::Phylo::PAML::ModelResult(3)

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

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