Ewan Birney


Bio::Tree::RandomFactory - TreeFactory for generating Random Trees


  use Bio::Tree::RandomFactory
  my $factory = new Bio::Tree::RandomFactory( -samples => \@taxonnames,
                                              -maxcount => 10);

  # or for anonymous samples

  my $factory = new Bio::Tree::RandomFactory( -sample_size => 6, 
                                              -maxcount = 50);


Builds a random tree every time next_tree is called or up to -maxcount times.

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


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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:


AUTHOR - Jason Stajich

Email jason@bioperl.org


Matthew Hahn, <matthew.hahn@duke.edu>


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 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    :


 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   : add_Mutations
 Usage   : $factory->add_Mutations($tree, $mutcount);
 Function: Adds mutations to a tree via a random process weighted by 
           branch length (it is a poisson distribution 
                          as part of a coalescent process) 
 Returns : none
 Args    : $tree - Bio::Tree::TreeI 
           $nummut - number of mutations


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


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


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


 Title   : attach_EventHandler
 Usage   : $parser->attatch_EventHandler($handler)
 Function: Adds an event handler to listen for events
 Returns : none
 Args    : Bio::Event::EventHandlerI


 Title   : _eventHandler
 Usage   : private
 Function: Get the EventHandler
 Returns : Bio::Event::EventHandlerI
 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)