Bio::Phylo::Generator - Generator of tree topologies
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;
The generator module is used to simulate trees under various models.
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
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
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.
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
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
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
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
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
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.
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
To install Bio::Phylo, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Phylo
CPAN shell
perl -MCPAN -e shell install Bio::Phylo
For more information on module installation, please visit the detailed CPAN module installation guide.