Bio::PopGen::Simulation::Coalescent(3pm)		User Contributed Perl Documentation		  Bio::PopGen::Simulation::Coalescent(3pm)

NAME

       Bio::PopGen::Simulation::Coalescent - A Coalescent simulation factory

SYNOPSIS

	   use Bio::PopGen::Simulation::Coalescent;
	   my @taxonnames = qw(SpeciesA SpeciesB SpeciesC SpeciesD);
	   my $sim1 = Bio::PopGen::Simulation::Coalescent->new(-samples => @taxonnames);

	   my $tree = $sim1->next_tree;

	   # add 20 mutations randomly to the tree
	   $sim1->add_Mutations($tree,20);

	   # or for anonymous samples

	   my $sim2 = Bio::PopGen::Simulation::Coalescent->new( -sample_size => 6,
								-maxcount => 50);
	   my $tree2 = $sim2->next_tree;
	   # add 20 mutations randomly to the tree
	   $sim2->add_Mutations($tree2,20);

DESCRIPTION

       Builds a random tree every time next_tree is called or up to -maxcount times with branch lengths and provides the ability to randomly add
       mutations onto the tree with a probabilty proportional to the branch lengths.

       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.

       This module was previously named Bio::Tree::RandomTree

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich, Matthew Hahn
       Email jason-at-bioperl-dot-org Email matthew-dot-hahn-at-duke-dot-edu

APPENDIX

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

   new
	Title	: new
	Usage	: my $obj = Bio::PopGen::Simulation::Coalescent->new();
	Function: Builds a new Bio::PopGen::Simulation::Coalescent object
	Returns : an instance of Bio::PopGen::Simulation::Coalescent
	Args	: -samples => arrayref of sample names
		  OR
		  -sample_size=> number of samples (samps will get a systematic name)
		  -maxcount   => [optional] maximum number of trees to provide

   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

   add_Mutations
	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
		  $precision - optional # of digits for precision

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

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

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

   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)

perl v5.14.2							    2012-03-02				  Bio::PopGen::Simulation::Coalescent(3pm)