TABLE 1.

Tools used in microbial ecology to describe and compare microbial communities

ToolApplicationInputReference
DOTUR/FastGroupAssigns sequences to OTUs based on genetic distance between sequences and constructs rarefaction curves and collector's curves for richness and diversity estimatorsDistance matrix20, 23
SONSCalculates collector's curves for estimates of the fraction and richness of OTUs shared between communitiesOTU designationThis study
LIBSHUFF/∫-LIBSHUFFUses the Cramer-von Mises statistic to test whether the structures of two communities are the same, different, or subsets of one anotherDistance matrix22, 24
TreeClimberImplements a parsimony-based test to determine whether the community structures of two or more communities are significantly differentPhylogenetic tree16, 18, 21
UniFracCompares the phylogenetic distances between pairs of communities to describe the similarity of their structuresPhylogenetic tree14
AMOVAUses an analysis of variance-type formulation to determine whether the genetic diversities of two or more community structures are significantly differentDistance matrix1, 10, 18