Interpretation Shannon and Simpson index

[colinbrislawn (Colin J Brislawn)]

@Wen

Is that analysis correct? Is the Simpson index calculated by Qiime2 the "normal" one and not the Simpson inverse?

Yes! The 0.95 and 0.99 Simpson index are the chance of drawing two different features from your sample, and not the inverse Simpson index.

@Wen

I understand that the values ​​I obtained for the Shannon index indicate that there is a high richness and homogeneity in the samples. On the other hand, the Simpson index tells me basically the same thing (high richness, but no species dominance). Is that analysis correct?

Almost... Both Shannon and Simpson measure a composite of richness and evenness. This matches your observation: one sample has higher alpha diversity (0.99 and 7.03) and one sample is slightly lower (3.98 and 0.95).

If you want to measure richness and evenness separately, check out this list of alpha metrics:

Alpha and Beta Diversity Explanations and Commands

About the Alpha and Beta Diversity Analysis Tutorial This Alpha and Beta Diversity Community Tutorial (run using QIIME 2017.12) walks you through analyzing the alpha and beta diversity of a sample dataset. Below you will find a link to a small test dataset to download and use in this tutorial. Files used in tutorial The following files, derived from the Moving Pictures tutorial, are used in this document. table.qza rooted-tree.qza Alpha Diversity Analysis The alpha and alpha-phylogenetic …

P.S. You are making good progress and asking all the right questions!