NAME

Bio::Phylo::Generator - Generates random trees.

SYNOPSIS

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

 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',
           );
 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',
           );
 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.

FORUM

CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo

BUGS

Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:

$Id: Generator.pm 1185 2006-05-26 09:04:17Z rvosa $

AUTHOR

Rutger A. Vos,

email: rvosa@sfu.ca

web page: http://www.sfu.ca/~rvosa/

ACKNOWLEDGEMENTS

The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.

COPYRIGHT & LICENSE

Copyright 2005 Rutger A. Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.