Alpha Diversity Metrics - Drive5

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See also Alpha diversity alpha_div command alpha_div_rare command beta_div command Interpreting diversity metrics Recommended alpha and beta metrics Comparing alpha diversity between groups Statistical significance of diversity differences

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.
mirror OTUs See mirror estimator .
FE OTUs See singleton-free estimator .
chao1 OTUs Chao-1 estimator, calculated as N + S 2 / (2 D) 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 f 2 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 d ifferent OTUs. Calculated as 1 - simpson.
equitability ? Also called Peilou's evenness. 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.
Reseek Structure alignment and search More accurate than TM-align, DALI and Foldseek Open-source USEARCH Fast sequence search, clustering, amplicon OTU and ASV analysis MUSCLE v5 State of the art MSA Recent updates 🔎 Reseek structure searchAFDB, BFVD & PDB > 📝 Preprint shows structure E-values wrong by orders of magnitude > 🧬 Assembly and search for entire SRA > 🚀 Open-source USEARCH > 🎯 Looking for new projects / collaborations > 1sco Search the AlphaFold DB online in seconds >

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