Christopher Fields > BioPerl > Bio::PopGen::Simulation::Coalescent

Download:
BioPerl-1.6.924.tar.gz

Dependencies

Annotate this POD

CPAN RT

New  9
Open  4
View/Report Bugs
Module Version: 1.006924   Source  

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

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)
syntax highlighting: