Understanding PERMANOVA QIIME2 Statistics for Beta Diversity

[Nicholas_Bokulich]

Hi @LVC,
This topic has a number of links to topics discussing PERMANOVA interpretation, etc, so I recommend taking a look here:

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@LVC

From my diagram above I am taking this to mean the statistics are referring to the difference between the within distances observed for A and the within distances observed for B (comparison 1) in the diagram. Is this correct?

Great diagram! PERMANOVA is really testing all 3 comparisons — basically, a significant result is telling you that the within-group distances of at least one group are less than the between-group distances for all groups.

@LVC

there was a Monte Carlo permutations 999 option in QIIME 1 previously but what should I be using in QIIME 2?

This is controlled by the --p-permutation parameter.

Good luck!