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Manual Reference Pages  -  BIO::PHYLO::GENERATOR (3)

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NAME

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

CONTENTS

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:

<B>Rutger A VosB>, <B>Jason CaravasB>, <B>Klaas HartmannB>, <B>Mark A JensenB> and <B>Chase MillerB>, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics <B>12B>:63. <http://dx.doi.org/10.1186/1471-2105-12-63>

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perl v5.20.3 BIO::PHYLO::GENERATOR (3) 2014-02-08

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