AMOVA distance matrix of OTU or sample?

I am running AMOVA using mothur and ade4.
I noticed the distance matrix input of mothur is the distance matrix between samples, while the distance matrix input for ade4 is between “OTUs”.
Therefore they generated completely different result.
Dose anyone look into the difference between the two algorithms? Thanks!

amova was created to look at molecular differences between populations, but it’s use in microbial ecology is use to look at differences between samples. So you are correct that they are doing different things (thought i’d bet you could get amova in ade4 to do samples by mar=2, haven’t tested).

Personally, I use permanova to compare my groups of samples (adonis in vegan)