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Bio::Tree::RandomFactory.3pm

NAME

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

SYNOPSIS

   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;
 
 

DESCRIPTION

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 ...

FEEDBACK

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/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason-AT-bioperl.org

CONTRIBUTORS

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

APPENDIX

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

new

  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
 
 

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)