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


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


           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

           # 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


       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


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AUTHOR - Jason Stajich, Matthew Hahn

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


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

        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
                  -sample_size=> number of samples (samps will get a systematic name)
                  -maxcount   => [optional] maximum number of trees to provide

        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

        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

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

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

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

        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)