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Manual Reference Pages  -  BIO::POPGEN::SIMULATION::COALESCENT (3)

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NAME

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

CONTENTS

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)



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perl v5.20.3 BIO::POPGEN::SIMULATION::COALESCENT (3) 2016-04-05

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