bio::phylonetwork::randomfactory(3pm) [debian man page]
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)
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Bio::Tree::RandomFactory(3pm) User Contributed Perl Documentation Bio::Tree::RandomFactory(3pm) NAME
Bio::Tree::RandomFactory - TreeFactory for generating Random Trees SYNOPSIS
use Bio::Tree::RandomFactory my @taxonnames; my $factory = Bio::Tree::RandomFactory->new( -taxa => @taxonnames, -maxcount => 10); # or for anonymous samples my $factory = Bio::Tree::RandomFactory->new( -num_taxa => 6, -maxcount => 50); my $tree = $factory->next_tree; DESCRIPTION
Builds a random tree every time next_tree is called or up to -maxcount times. This module was originally written for Coalescent simulations see Bio::PopGen::Simulation::Coalescent. I've left the next_tree method intact although it is not generating random trees in the phylogenetic sense. I would be happy for someone to provide alternative implementations which can be used here. As written it will generate random topologies but the branch lengths are built from assumptions in the coalescent and are not appropriate for phylogenetic analyses. This algorithm is based on the make_tree algorithm from Richard Hudson 1990. Hudson, R. R. 1990. Gene genealogies and the coalescent process. Pp. 1-44 in D. Futuyma and J. Antonovics, eds. Oxford surveys in evolutionary biology. Vol. 7. Oxford University Press, New York Sanderson, M ... FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Jason Stajich Email jason-AT-bioperl.org CONTRIBUTORS
Matthew Hahn, <matthew.hahn@duke.edu> Mike Sanderson APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : my $factory = Bio::Tree::RandomFactory->new(-samples => @samples, -maxcount=> $N); Function: Initializes a Bio::Tree::RandomFactory object Returns : Bio::Tree::RandomFactory Args : -nodetype => Type of Nodes to create [default Bio::Tree::Node] -maxcount => [optional] Maximum num trees to create -randtype => Type of random trees so far support - yule/backward_yule/BY [default] - forward_yule/FY - birthdeath_forward/BDF - birthdeath_backwards/BDB ONE of the following must be specified -taxa => $arrayref of taxa names -num_taxa => integer indicating number of taxa in the tree next_tree Title : next_tree Usage : my $tree = $factory->next_tree Function: Returns a random tree based on the initialized number of nodes NOTE: if maxcount is not specified on initialization or set to a valid integer, subsequent calls to next_tree will continue to return random trees and never return undef Returns : Bio::Tree::TreeI object Args : none maxcount Title : maxcount Usage : $obj->maxcount($newval) Function: Returns : Maxcount value Args : newvalue (optional) reset_tree_count Title : reset_tree_count Usage : $factory->reset_tree_count; Function: Reset the tree counter Returns : none Args : none taxa Title : taxa Usage : $obj->taxa($newval) Function: Set the leaf node names Returns : value of taxa Args : Arrayref of Taxon names num_taxa Title : num_taxa Usage : $obj->num_taxa($newval) Function: Get the number of Taxa Returns : value of num_taxa Args : none random Title : random Usage : my $rfloat = $node->random($size) Function: Generates a random number between 0 and $size This is abstracted so that someone can override and provide their own special RNG. This is expected to be a uniform RNG. Returns : Floating point random Args : $maximum size for random number (defaults to 1) random_tree_method Title : random_tree_method Usage : $obj->random_tree_method($newval) Function: Example : Returns : value of random_tree_method (a scalar) Args : on set, new value (a scalar or undef, optional) nodetype Title : nodetype Usage : $obj->nodetype($newval) Function: Example : Returns : value of nodetype (a scalar) Args : on set, new value (a scalar or undef, optional) perl v5.14.2 2012-03-02 Bio::Tree::RandomFactory(3pm)