USEARCH manual

Alpha diversity metrics

While many of these alpha diversity metrics are commonly used in OTU analysis, in fact many of them are invalid or hard to interpret for OTUs constructed from NGS amplicon reads.

Diversity metrics

Name

Units

Description

richness

OTUs

Number of OTUs with at least one read for the sample.

chao1	OTUs	Chao-1 estimator, calculated as N + S² / (2 D²) where N is the number of OTUs, S is the number of singleton OTUs and D is the number of doublet OTUs, i.e. OTUs with abundance 2.
shannon_2	bits	Shannon index (logs to base 2).
shannon_e	nats	Shannon index (logs to base e).
shannon_10	dits	Shannon index (logs to base 10).
jost	OTUs	Jost index of order q where q is specified by the -jostq command-line option, default 1.5.
jost1	OTUs	Jost index of order 1, the effective number of species given by the Shannon index.

Evenness metrics

Name	Units	Description
simpson	Probability	Simpson index, calculated as the sum over OTUs of f² where f is the frequency of the OTU. It is the probability that two randomly selected reads will belong to the same OTU. A value close to 1 indicates that a single large OTU dominates the sample, small values indicate that the reads are distributed over many OTUs.
dominance	Probability	Probability that two randomly selected reads will belong to different OTUs. Calculated as 1 – simpson.
equitability	?	Entropy (Shannon index) divided by the logarithm of the number of OTUs. Value of 1 indicates perfectly even (equal abundances), small values indicate a highly skewed abundance distribution.
robbins	Frequency	Robbins index, calculated as S / (N + 1) where S is the number of singleton OTUs and N is the total number of OTUs.
berger_parker	Frequency	Berger-Parker index. Frequency of the most abundant OTU. A value close to 1 indicates that a single large OTU dominates the sample, small values indicate that the reads are distributed over many OTUs.

Other

Name	Units	Description
reads	Reads	Total number of reads for the sample.