/ 
BioPerl-1.6.920
River stage two • 61 direct dependents • 66 total dependents
/ Bio::PopGen::Simulation::Coalescent

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)