Bio::PhyloNetwork::RandomFactory(3) Module to generate random


use strict;
use warnings;
use Bio::PhyloNetwork;
use Bio::PhyloNetwork::RandomFactory;
# Will generate at random all the 66 binary tree-child phylogenetic
# networks with 3 leaves
my $factory=Bio::PhyloNetwork::RandomFactory->new(-numleaves=>3,-norepeat=>1);
my @nets;
for (my $i=0; $i<66; $i++) {
my $net=$factory->next_network();
push @nets,$net;
print "".(scalar @nets).": ".$net->eNewick()."\n";


Builds a random (binary tree-child) phylogenetic network each time next_network is called.


Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es


The rest of the documentation details each of the object methods.


 Title   : new
 Usage   : my $factory = new Bio::PhyloNetwork::RandomFactory();
 Function: Creates a new Bio::PhyloNetwork::RandomFactory
 Returns : Bio::PhyloNetwork::RandomFactory
 Args    : -numleaves => integer
           -leaves => reference to an array (of leaves names)
           -numhybrids => integer [optional]
           -norepeat => boolean [optional]

Returns a Bio::PhyloNetwork::RandomFactory object. Such an object will create random binary tree-child phylogenetic networks each time next_network is called.

If the parameter -leaves=>\@leaves is given, then the set of leaves of these networks will be @leaves. If it is given the parameter -numleaves=>$numleaves, then the set of leaves will be ``l1''...``l$numleaves''.

If the parameter -numhybrids=>$numhybrids is given, then the generated networks will have exactly $numhybrids hybrid nodes. Note that, necessarily, $numhybrids < $numleaves. Otherwise, the number of hybrid nodes will be chosen at random for each call of next_network.

If the parameter -norepeat=>1 is given, then successive calls of next_network will give non-isomorphic networks.


 Title   : next_network
 Usage   : my $net=$factory->next_network()
 Function: returns a random network
 Returns : Bio::PhyloNetwork
 Args    : none