Provided by: libbio-perl-perl_1.7.2-3_all bug

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://github.com/bioperl/bioperl-live/issues

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)