joey711/phyloseq — Issue #51: Add Fast UniFrac to UniFrac() method, make default
Author: joey711
Created: 2011-11-16 21:07:50+00:00
State: open
Labels: Feature

A more-efficient, matrix-based version of UniFrac is described in:

http://www.nature.com/ismej/journal/v4/n1/abs/ismej200997a.html

It converts the tree into a matrix of branches, their lengths, and the samples that descend from each; and then performs all of the UniFrac calculations on that matrix. This is apparently much faster than traversing the tree for each step of the calculation.

If this works and gives identical results, it should be set as the default option, along with the option to parallelize it.