Bio::Tree::RandomFactory - TreeFactory for generating Random Trees use Bio::Tree::RandomFactory my @taxonnames; my $factory = new Bio::Tree::RandomFactory( -taxa => \@taxonnames, -maxcount => 10); # or for anonymous samples my $factory = new Bio::Tree::RandomFactory( -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 ...

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 the web: http://bugzilla.bioperl.org/ Email jason-AT-bioperl.org Matthew Hahn, <matthew.hahn@duke.edu> Mike Sanderson The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $factory = new Bio::Tree::RandomFactory(-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

next_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

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

reset_tree_count
Title : reset_tree_count Usage : $factory->reset_tree_count; Function: Reset the tree counter Returns : none Args : none

taxa
Title : taxa Usage : $obj->taxa($newval) Function: Set the leaf node names Returns : value of taxa Args : Arrayref of Taxon names

num_taxa
Title : num_taxa Usage : $obj->num_taxa($newval) Function: Get the number of Taxa Returns : value of num_taxa Args : none

random
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)

random_tree_method
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)

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