/ 
Bio-Phylo-0.19
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
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
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

SEE ALSO

Bio::Phylo::Manual

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

REVISION

$Id: Generator.pm 1235 2010-03-02 16:11:07Z rvos $