bio::phylonetwork::treefactoryx(3pm) [debian man page]
Bio::PhyloNetwork::TreeFactoryX(3pm) User Contributed Perl Documentation Bio::PhyloNetwork::TreeFactoryX(3pm) NAME
Bio::PhyloNetwork::TreeFactoryX - Module to sequentially generate Phylogenetic Trees SYNOPSIS
use strict; use warnings; use Bio::PhyloNetwork; use Bio::PhyloNetwork::TreeFactory; # Will generate sequentially all the 15 binary phylogetic # trees with 4 leaves my $factory=Bio::PhyloNetwork::TreeFactory->new(-numleaves=>4); my @nets; while (my $net=$factory->next_network()) { push @nets,$net; print "".(scalar @nets).": ".$net->eNewick()." "; } DESCRIPTION
Sequentially builds a (binary) phylogenetic tree 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 $factory = new Bio::PhyloNetwork::TreeFactory(); Function: Creates a new Bio::PhyloNetwork::TreeFactory Returns : Bio::PhyloNetwork::RandomFactory Args : -numleaves => integer OR -leaves => reference to an array (of leaves names) Returns a Bio::PhyloNetwork::TreeFactory object. Such an object will sequentially create binary phylogenetic trees each time next_network is called. If the parameter -leaves=>@leaves is given, then the set of leaves of these networks will be @leaves. If it is given the parameter -numleaves=>$numleaves, then the set of leaves will be "l1"..."l$numleaves". next_network Title : next_network Usage : my $net=$factory->next_network() Function: returns a tree Returns : Bio::PhyloNetwork Args : none perl v5.14.2 2012-03-02 Bio::PhyloNetwork::TreeFactoryX(3pm)
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Bio::PhyloNetwork::RandomFactory(3pm) User Contributed Perl Documentation Bio::PhyloNetwork::RandomFactory(3pm) NAME
Bio::PhyloNetwork::RandomFactory - Module to generate random Phylogenetic Networks 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()." "; } 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 perl v5.14.2 2012-03-02 Bio::PhyloNetwork::RandomFactory(3pm)