Ewan Birney

NAME

Bio::Tree::Statistics - Calculate certain statistics for a Tree

SYNOPSIS

Give standard usage here

DESCRIPTION

This object is a place to accumulate routines for calculating various tree statistics from population genetic and phylogenetic methods.

Currently Fu and Li's D is implemented. Tajima's D planned.

References forthcoming.

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/MailList.shtml  - About the mailing lists

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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

AUTHOR - Jason Stajich

Email jason@bioperl.org

CONTRIBUTORS

Matt Hahn <matthew.hahn@duke.duke>

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 = new Bio::Tree::Statistics();
 Function: Builds a new Bio::Tree::Statistics object 
 Returns : Bio::Tree::Statistics
 Args    :

fu_and_li_D

 Title   : fu_and_li_D
 Usage   : my $D = $statistics->fu_an_li_D($tree,$nummut);
 Function:
           For this we assume that the tree is made up of
           Bio::Tree::AlleleNode's which contain markers and alleles
           each marker is a 'mutation' 
 Returns : Fu and Li's D statistic for this Tree
 Args    : $tree - Bio::Tree::TreeI which contains Bio::Tree::AlleleNodes