Table 1 Tools used to describe and compare microbial communities.
From: A statistical toolbox for metagenomics: assessing functional diversity in microbial communities
Tool | Application | Input | Reference |
|---|---|---|---|
DOTUR/MG-DOTUR | 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 or BLAST Table | [30] |
SONS | Generates collector's curves for estimates of the fraction and richness of OTUs shared between communities | OTU Designation | [56] |
∫-LIBSHUFF/MG-LIBSHUFF | Tests whether the structures of two communities are the same, different, or subsets of one another using the Cramer-von Mises statistic | Distance Matrix or BLAST Table | [31, 32] |
AMOVA/MG-AMOVA | Determines whether two or more communities differ significantly in genetic diversity using an analysis of variance-type formulation | Distance Matrix or BLAST Table | [33, 47, 48] |