Bio::PopGen::Simulation::Coalescent.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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)