Statistical analyses on UNIFRAC assigned distances


I calculated weighted and unweighted UNIFRAC distances from my sequences with the UniFrac command in mothur.
Now I would like to perform statistics on these distances. Normally, p values are calculated in the UniFrac command, however these p-values are, I think,
generated by comparing all sequences with each other (please correct me if I am wrong) and were not helpfull in my case (I would like to calculate differences between the clusters).
Could I use the AMOVA analyses in Mothur to calculate significant differences? Or do you have other suggestions?

Thank you for your help!

You can use unifrac, amova, homova, or anosim to compare these distances without a problem