Does QIIME2 have an equivalent of from qiime1?

Hi all,

I’m looking for an equivalent to from qiime1?

Does such a plugin exist? I’ve combed through the tutorials and while diversity supports group significance, I’m looking to compare sample significance.


Hi @William_G_Ryan! Have you had a chance to look at the docs? In particular, this section of the Moving Pictures Tutorial, and, the docs for q2-diversity.

:qiime2: :t_rex:

My apologies, I accidentally typed the wrong plugin name I’m referring to from qiime1.

Hey @William_G_Ryan, no difference, the same two links I sent have you covered. In fact, the MP Tutorial has a worked example of beta group significance. :open_book:

I understand. However, I’m not looking to compare beta group significance. I’m looking to compare between samples, not groups of samples. If you look at, it requires an OTU table and tree and does pairwise comparisons between each sample and generates a p-value for each comparison with unifrac monte carlo simulations.

Beta group significance requires a group category parameter. If I attempt to use beta group significance with my sample names, it fails because they all unique samples names.

Hi @William_G_Ryan,

The short answer is that there isn’t a re-implementation in QIIME 2 for determining if pairwise beta diversity calculations are significant against some null hypothesis.

I think, in general, this is because there’s been movement toward larger studies that make per sample pairwise comparisons somewhat moot in the face of larger, cross sectional data. At this point, I would discourage this approach to the data. If you need a specific test for paired samples in group, the pairwise sample tutorial from the longitudinal plugin may be helpful.

I think the best advice is to work with group-level rather than per-sample comparisons.


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