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 $sim1->add_Mutations($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);
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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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 OR -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) Function: Returns : Maxcount value Args : newvalue (optional)
Title : samples Usage : $obj->samples($newval) Function: Example : Returns : value of samples Args : newvalue (optional)
Title : sample_size Usage : $obj->sample_size($newval) Function: 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)