Using UniFrac

Hi my name is Eduardo

Im working with 16S data and I have a doubt related with unifrac.weighted. The articles I found said this protocol (UniFrac) used phylogenetic information to generate a distance matrix and then compare the structure of communities, so if I generate a tree with distances of bray-curtis (with dist.shared) my result could be considered correct? I would like to understand how this command in mothur work with data that is not UniFrac distance
Also I would like to know if there is a way to get the representative sequences of OTUs defined through phylotype?

Thanks in advance!

Bray-Curtis is a great option to replace weigthed UniFrac if you want your analysis based on OTUs or phylotypes.