RT Journal Article
SR Electronic
T1 EMDUNIFRAC: EXACT LINEAR TIME COMPUTATION OF THE UNIFRAC METRIC AND IDENTIFICATION OF DIFFERENTIALLY ABUNDANT ORGANISMS
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 087171
DO 10.1101/087171
A1 McClelland, Jason
A1 Koslicki, David
YR 2016
UL http://biorxiv.org/content/early/2016/11/14/087171.abstract
AB Both the weighted and unweighted Unifrac distances have been very successfully employed to assess if two communities differ, but do not give any information about how two communities differ. We take advantage of recent observations that the Unifrac metric is equivalent to the so-called earth moverâ€™s distance (also known as the Kantorovich-Rubinstein metric) to develop an algorithm that not only computes the Unifrac distance in linear time and space, but also simultaneously finds which operational taxonomic units are responsible for the observed differences between samples. This allows the algorithm, called EMDUnifrac, to determine why given samples are different, not just if they are different, and with no added computational burden. EMDUnifrac can be utilized on any distribution on a tree, and so is particularly suitable to analyzing both operational taxonomic units derived from amplicon sequencing, as well as community profiles resulting from classifying whole genome shotgun metagenomes. The EMDUnifrac source code (written in python) is freely available at: https://github.com/dkoslicki/EMDUnifrac.