Bio::Tools::Phylo::PAML::ModelResult - A container for NSSite Model Result from PAML # get a ModelResult from a PAML::Result object use Bio::Tools::Phylo::PAML; my $paml = new Bio::Tools::Phylo::PAML(-file => 'mlc'); my $result = $paml->next_result; foreach my $model ( $result->get_model_results ) { print $model->model_num, " ", $mode->model_description, "\n"; print $model->kappa, "\n"; print $model->run_time, "\n"; } Describe the object here

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/MailList.shtml - About the mailing lists

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: http://bugzilla.bioperl.org/ Email jason@open-bio.org Describe contact details here Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::Tools::Phylo::PAML::ModelResult(); 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 -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 '**'

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
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>

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)