/ 
Bio-Phylo-0.26
River stage two • 9 direct dependents • 18 total dependents
/ Bio::Phylo::Generator

NAME

Bio::Phylo::Generator - Generator of tree topologies

SYNOPSIS

use Bio::Phylo::Factory;
my $fac = Bio::Phylo::Factory->new;
my $gen = $fac->create_generator;
my $trees = $gen->gen_rand_pure_birth( 
    '-tips'  => 10, 
    '-model' => 'yule',
    '-trees' => 10,
);

# prints 'Bio::Phylo::Forest'
print ref $trees;

DESCRIPTION

The generator module is used to simulate trees under the Yule, Hey, or equiprobable model.

METHODS

CONSTRUCTOR

new()

Generator constructor.

Type    : Constructor
Title   : new
Usage   : my $gen = Bio::Phylo::Generator->new;
Function: Initializes a Bio::Phylo::Generator object.
Returns : A Bio::Phylo::Generator object.
Args    : NONE

GENERATOR

gen_rand_pure_birth()

This method generates a Bio::Phylo::Forest object populated with Yule/Hey trees.

 Type    : Generator
 Title   : gen_rand_pure_birth
 Usage   : my $trees = $gen->gen_rand_pure_birth(
               '-tips'  => 10, 
               '-model' => 'yule',
               '-trees' => 10,
           );
 Function: Generates markov tree shapes, 
           with branch lengths sampled 
           from a user defined model of 
           clade growth, for a user defined
           number of tips.
 Returns : A Bio::Phylo::Forest object.
 Args    : -tips  => number of terminal nodes,
           -model => either 'yule' or 'hey',
           -trees => number of trees to generate
	   Optional: -factory => a Bio::Phylo::Factory object
gen_exp_pure_birth()

This method generates a Bio::Phylo::Forest object populated with Yule/Hey trees whose branch lengths are proportional to the expected waiting times (i.e. not sampled from a distribution).

 Type    : Generator
 Title   : gen_exp_pure_birth
 Usage   : my $trees = $gen->gen_exp_pure_birth(
               '-tips'  => 10, 
               '-model' => 'yule',
               '-trees' => 10,
           );
 Function: Generates markov tree shapes, 
           with branch lengths following 
           the expectation under a user 
           defined model of clade growth, 
           for a user defined number of tips.
 Returns : A Bio::Phylo::Forest object.
 Args    : -tips  => number of terminal nodes,
           -model => either 'yule' or 'hey'
           -trees => number of trees to generate
	   Optional: -factory => a Bio::Phylo::Factory object
gen_equiprobable()

This method draws tree shapes at random, such that all shapes are equally probable.

 Type    : Generator
 Title   : gen_equiprobable
 Usage   : my $trees = $gen->gen_equiprobable( 
               '-tips'  => 10, 
               '-trees' => 5,
           );
 Function: Generates an equiprobable tree 
           shape, with branch lengths = 1;
 Returns : A Bio::Phylo::Forest object.
 Args    : -tips  => number of terminal nodes,
           -trees => number of trees to generate,
	   Optional: -factory => a Bio::Phylo::Factory object

SEE ALSO

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.

REVISION

$Id: Generator.pm 1274 2010-03-17 16:03:26Z rvos $