Jost diversity index
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11-Aug-2018 New paper describes octave plots for visualizing alpha diversity.

12-Jun-2018 New paper shows that one in five taxonomy annotations in SILVA and Greengenes are wrong.

18-Apr-2018 New paper shows that taxonomy prediction accuracy is <50% for V4 sequences.

05-Oct-2017 PeerJ paper shows low accuracy of closed- and open-ref. QIIME OTUs.

22-Sep-2017 New paper shows 97% threshold is wrong, OTUs should be 99% full-length 16S, 100% for V4.

UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.



Jost diversity index

See also
alpha_div command
 Alpha diversity metrics
 Effective number of species

In a 2010 paper, Chao, Chui and Jost describe a family of metrics based on Hill numbers with a single parameter (q) that determines how abundance is weighted. I call these Jost indexes of order q. The numerical value of the metric for any q is an effective number of species.

The parameter q is the power to which the species frequencies are raised. Higher values of q thus give lower weights to low-abundance species. With q=0 the Jost index is exactly equivalent to richness. With q=1, the Jost index is the effective number of species given by the Shannon entropy. The q parameter can take real values, not just integers, which allows intermediate metrics with different weightings of abundance.
Chao, Chui and Jost (2010)