Hello,

I have been encountering a puzzling phenomenon when performing PERMANOVA tests with `beta-group-significance`

in Qiime2 (v2018.2). The p-value for tests performed in Qiime2 are consistently lower than the results from the `adonis`

function in the R package vegan. This is true for several data sets, but I have documented the analysis for one dataset at: https://github.com/maggimars/MicrobiomeSelection.

For this particular example, the `adonis`

p-value for between group differences is 0.023, the R-squared is 0.506 and the F.Model is 2.0557. When the same analysis is repeated with Qiime2 `beta-group-significance`

, the p-value is 0.003 and the psuedo-F is 3.0469.

I was under the impression that `adonis`

and PERMANOVA in Qiime2 should yield the same results. Is there a simple reason why I may be seeing different results with the two methods?

Thank you,

Maggi