NAME

       Bio::PopGen::Simulation::Coalescent - A Coalescent simulation factory

SYNOPSIS

           use Bio::PopGen::Simulation::Coalescent;
           my @taxonnames = qw(SpeciesA SpeciesB SpeciesC SpeciesD);
           my $sim1 = Bio::PopGen::Simulation::Coalescent->new(-samples => \@taxonnames);

           my $tree = $sim1->next_tree;

           # add 20 mutations randomly to the tree
           $sim1->add_Mutations($tree,20);

           # or for anonymous samples

           my $sim2 = Bio::PopGen::Simulation::Coalescent->new( -sample_size => 6,
                                                                -maxcount => 50);
           my $tree2 = $sim2->next_tree;
           # add 20 mutations randomly to the tree
           $sim2->add_Mutations($tree2,20);

DESCRIPTION

       Builds a random tree every time next_tree is called or up to -maxcount times with branch
       lengths and provides the ability to randomly add mutations onto the tree with a probabilty
       proportional to the branch lengths.

       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.

       This module was previously named Bio::Tree::RandomTree

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, Matthew Hahn

       Email jason-at-bioperl-dot-org Email matthew-dot-hahn-at-duke-dot-edu

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   new
        Title   : new
        Usage   : my $obj = Bio::PopGen::Simulation::Coalescent->new();
        Function: Builds a new Bio::PopGen::Simulation::Coalescent object
        Returns : an instance of Bio::PopGen::Simulation::Coalescent
        Args    : -samples => arrayref of sample names
                  OR
                  -sample_size=> number of samples (samps will get a systematic name)
                  -maxcount   => [optional] maximum number of trees to provide

   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

   add_Mutations
        Title   : add_Mutations
        Usage   : $factory->add_Mutations($tree, $mutcount);
        Function: Adds mutations to a tree via a random process weighted by
                  branch length (it is a poisson distribution
                                 as part of a coalescent process)
        Returns : none
        Args    : $tree - Bio::Tree::TreeI
                  $nummut - number of mutations
                  $precision - optional # of digits for precision

   maxcount
        Title   : maxcount
        Usage   : $obj->maxcount($newval)
        Function:
        Returns : Maxcount value
        Args    : newvalue (optional)

   samples
        Title   : samples
        Usage   : $obj->samples($newval)
        Function:
        Example :
        Returns : value of samples
        Args    : newvalue (optional)

   sample_size
        Title   : sample_size
        Usage   : $obj->sample_size($newval)
        Function:
        Example :
        Returns : value of sample_size
        Args    : newvalue (optional)

   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)