TABLE 1.

Tools used in microbial ecology to describe and compare microbial communities

Tool	Application	Input	Reference
DOTUR/FastGroup	Assigns sequences to OTUs based on genetic distance between sequences and constructs rarefaction curves and collector's curves for richness and diversity estimators	Distance matrix	20, 23
SONS	Calculates collector's curves for estimates of the fraction and richness of OTUs shared between communities	OTU designation	This study
LIBSHUFF/∫-LIBSHUFF	Uses the Cramer-von Mises statistic to test whether the structures of two communities are the same, different, or subsets of one another	Distance matrix	22, 24
TreeClimber	Implements a parsimony-based test to determine whether the community structures of two or more communities are significantly different	Phylogenetic tree	16, 18, 21
UniFrac	Compares the phylogenetic distances between pairs of communities to describe the similarity of their structures	Phylogenetic tree	14
AMOVA	Uses an analysis of variance-type formulation to determine whether the genetic diversities of two or more community structures are significantly different	Distance matrix	1, 10, 18