Bio::Tree::RandomFactory - TreeFactory for generating Random Trees
use Bio::Tree::RandomFactory my @taxonnames; my $factory = Bio::Tree::RandomFactory->new( -taxa => \@taxonnames, -maxcount => 10); # or for anonymous samples my $factory = Bio::Tree::RandomFactory->new( -num_taxa => 6, -maxcount => 50); my $tree = $factory->next_tree;
Builds a random tree every time next_tree is called or up to -maxcount times.
This module was originally written for Coalescent simulations see Bio::PopGen::Simulation::Coalescent. I've left the next_tree method intact although it is not generating random trees in the phylogenetic sense. I would be happy for someone to provide alternative implementations which can be used here. As written it will generate random topologies but the branch lengths are built from assumptions in the coalescent and are not appropriate for phylogenetic analyses.
This algorithm is based on the make_tree algorithm from Richard Hudson 1990.
Hudson, R. R. 1990. Gene genealogies and the coalescent process. Pp. 1-44 in D. Futuyma and J. Antonovics, eds. Oxford surveys in evolutionary biology. Vol. 7. Oxford University Press, New York
Sanderson, M ...
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $factory = Bio::Tree::RandomFactory->new(-samples => \@samples, -maxcount=> $N); Function: Initializes a Bio::Tree::RandomFactory object Returns : Bio::Tree::RandomFactory Args : -nodetype => Type of Nodes to create [default Bio::Tree::Node] -maxcount => [optional] Maximum num trees to create -randtype => Type of random trees so far support - yule/backward_yule/BY [default] - forward_yule/FY - birthdeath_forward/BDF - birthdeath_backwards/BDB ONE of the following must be specified -taxa => $arrayref of taxa names -num_taxa => integer indicating number of taxa in the tree
Title : next_tree Usage : my $tree = $factory->next_tree Function: Returns a random tree based on the initialized number of nodes NOTE: if maxcount is not specified on initialization or set to a valid integer, subsequent calls to next_tree will continue to return random trees and never return undef Returns : Bio::Tree::TreeI object Args : none
Title : maxcount Usage : $obj->maxcount($newval) Function: Returns : Maxcount value Args : newvalue (optional)
Title : reset_tree_count Usage : $factory->reset_tree_count; Function: Reset the tree counter Returns : none Args : none
Title : taxa Usage : $obj->taxa($newval) Function: Set the leaf node names Returns : value of taxa Args : Arrayref of Taxon names
Title : num_taxa Usage : $obj->num_taxa($newval) Function: Get the number of Taxa Returns : value of num_taxa Args : none
Title : random Usage : my $rfloat = $node->random($size) Function: Generates a random number between 0 and $size This is abstracted so that someone can override and provide their own special RNG. This is expected to be a uniform RNG. Returns : Floating point random Args : $maximum size for random number (defaults to 1)
Title : random_tree_method Usage : $obj->random_tree_method($newval) Function: Example : Returns : value of random_tree_method (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : nodetype Usage : $obj->nodetype($newval) Function: Example : Returns : value of nodetype (a scalar) Args : on set, new value (a scalar or undef, optional)