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Christopher Fields > BioPerl > Bio::Tree::RandomFactory



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Module Version: 1.007002   Source  


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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AUTHOR - Jason Stajich ^



Matthew Hahn, <> Mike Sanderson


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)
 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)
 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)
 Example : 
 Returns : value of nodetype (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
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