ANOSIM output


I’m running the anosim function with a phylip formatted dist matrix and appropriate design file, but in the output file I’m only getting a single line comparing all of the groups. Is there a way to get the pairwise metrics as well as in the example?

I’ve tried looking at both a distance matrix of sequences and a design file that places the sequences into samples to see if there’s a difference between samples

as well as a distance matrix between samples and a design file that places each sample into one of two groups


mothur will first do a between-all-groups test for significant structuring, then if that structuring at that level is significant do the pairwise tests. What is the p-value on that one line you’re seeing? I’d expect that it’s >0.05 and so mothur isn’t going into the pairwise comparisons.

It’s an analogous approach to an ANOVA - an overall test for any significance before you step into the pairwise comparisons and have to worry about your false positive rate and multiple testing correction.

Thanks! Yes, the p-value was >0.05 (0.3)