what post hoc method Alpha diversity significance results Kruskal-Wallis (pairwise) test used in Qiime2?

[Mehrbod_Estaki]

Hi @Lei,

@Lei

1. FDR method of Benjamini and Hochberg were used for multiple comparisons in the Kruskal-Wallis pairwise test in Qiime2?

Correct! see here for confirmation

@Lei

2. Qiime2 also use Dunn’s tests as post hoc for Krustal-Wallis pairwise test?

Not quite, Q2 just uses the Kruskal-Wallis test again for pairwise comparisons. I believe the KW test is basically an extension of the Mann-Whitney test for multiple groups, so that may be more of an appropriate comparison than the Dunn's test. But I would imagine you would get nearly identical results.