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)