beta-diversity indices， which to choose？

[aipolly]

hello everyone！

There are several different indices which have been widely used in metagenomics for beta diverity, the clustering result show there is great difference between them. my thought is that there is no 'which one is best', but which fits your data better. However, I don't know which result to believe, Can you help me out?

[JamieHeather]

Each one really measures a different thing, but the question is whether that aspect of diversity is what you're interested in.

Have a read of Jost's Entropy and Diversity, I think that covers a lot of the ground very nicely.