Beta diversity: within and between group comparisons

Hello all,

I would like to clarify the output of qiime diversity beta-group-significance
I am looking for the “All between groups” and “All within groups” comparisons (using t-test pairwise) as well as the rest of the Unifrac distances group comparisons as you used to provide in QIIME 1.

Is it possible to do it through QIIME 2? or is the PERMANOVA pairwise analysis replacing this function?

Thank you very much for your support.


Hi @Daniela_Vargas!

Yes, the PERMANOVA test in beta-group-significance is QIIME 2’s replacement for the t-tests in QIIME 1’s script. PERMANOVA was actually available in QIIME 1’s script, along with other non-parametric multivariate statistics. In QIIME 2, beta-group-significance combines the functionality of those two scripts into a single command. PERMANOVA is a more statistically robust method than QIIME 1’s t-tests, so that’s why we’re not re-implementing the t-tests here.

The table at the top of the visualization’s page (titled “PERMANOVA results”) provides “global” results for PERMANOVA, i.e. applied to all groups. Pairwise PERMANOVA results are included at the bottom of the page.

Note: beta-group-significance also supports the ANOSIM test by passing --p-method anosim.


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