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Manual Reference Pages  -  BIO::PHYLONETWORK::RANDOMFACTORY (3)

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NAME

Bio::PhyloNetwork::RandomFactory - Module to generate random Phylogenetic Networks

CONTENTS

SYNOPSIS



 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";
 }



DESCRIPTION

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

AUTHOR

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

SEE ALSO

Bio::PhyloNetwork

APPENDIX

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

    new



 Title   : new
 Usage   : my $factory = new Bio::PhyloNetwork::RandomFactory();
 Function: Creates a new Bio::PhyloNetwork::RandomFactory
 Returns : Bio::PhyloNetwork::RandomFactory
 Args    : -numleaves => integer
            OR
           -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.

    next_network



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



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perl v5.20.3 BIO::PHYLONETWORK::RANDOMFACTORY (3) 2016-04-05

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