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 various models.

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 (default: 10),
           -model => either 'yule' or 'hey',
           -trees => number of trees to generate (default: 10)
	   Optional: -factory => a Bio::Phylo::Factory object

gen_rand_birth_death()

This method generates a Bio::Phylo::Forest object populated under a birth/death model

 Type    : Generator
 Title   : gen_rand_birth_death
 Usage   : my $trees = $gen->gen_rand_birth_death(
               '-tips'     => 10, 
               '-killrate' => 0.2,
               '-trees'    => 10,
           );
 Function: Generates trees where any growing lineage is equally
           likely to split at any one time, and is equally likely
	   to go extinct at '-killrate'
 Returns : A Bio::Phylo::Forest object.
 Args    : -tips  => number of terminal nodes (default: 10),
           -killrate => extinction over speciation rate (default: 0.2)
           -trees => number of trees to generate (default: 10)
	   Optional: -factory => a Bio::Phylo::Factory object
 Comments: Past extinction events are retained as unbranched internal
           nodes in the produced trees.

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 (default: 10),
           -model => either 'yule' or 'hey'
           -trees => number of trees to generate (default: 10)
	   Optional: -factory => a Bio::Phylo::Factory object

gen_coalescent()

This method generates coalescent trees for a given effective population size (popsize) and number of alleles (tips) such that the probability of coalescence in the previous generation for any pair of alleles is 1 / ( 2 * popsize ).

 Type    : Generator
 Title   : gen_coalescent
 Usage   : my $trees = $gen->gen_coalescent(
               '-tips'    => 10, 
               '-popsize' => 100,
               '-trees'   => 10,
           );
 Function: Generates coalescent trees.
 Returns : A Bio::Phylo::Forest object.
 Args    : -tips    => number of terminal nodes (default: 10)
           -popsize => effective population size (default: 100)
           -trees   => number of trees to generate (default: 10)
	   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 );
 Function: Generates an equiprobable tree 
           shape, with branch lengths = 1;
 Returns : A Bio::Phylo::Forest object.
 Args    : Optional: -tips  => number of terminal nodes (default: 10),
           Optional: -trees => number of trees to generate (default: 1),
	   Optional: -factory => a Bio::Phylo::Factory object

gen_balanced()

This method creates the most balanced topology possible given the number of tips

 Type    : Generator
 Title   : gen_balanced
 Usage   : my $trees = $gen->gen_balanced( '-tips'  => 10 );
 Function: Generates the most balanced topology
           possible, with branch lengths = 1;
 Returns : A Bio::Phylo::Forest object.
 Args    : Optional: -tips  => number of terminal nodes (default: 10),
           Optional: -trees => number of trees to generate (default: 1),
	   Optional: -factory => a Bio::Phylo::Factory object

gen_ladder()

This method creates a ladder tree for the number of tips

 Type    : Generator
 Title   : gen_ladder
 Usage   : my $trees = $gen->gen_ladder( '-tips'  => 10 );
 Function: Generates the least balanced topology
           (a ladder), with branch lengths = 1;
 Returns : A Bio::Phylo::Forest object.
 Args    : Optional: -tips  => number of terminal nodes (default: 10),
           Optional: -trees => number of trees to generate (default: 1),
	   Optional: -factory => a Bio::Phylo::Factory object

SEE ALSO

There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.

Bio::Phylo::Manual

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

CITATION

If you use Bio::Phylo in published research, please cite it:

Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63