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

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Module Version: 1.006924   Source  

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:

  https://github.com/bioperl/bioperl-live/issues

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)
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