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Christopher Fields
and 1 contributors


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)