From tree to clusters

How does mothur cut a tree (e.g. a UPGMA tree) at a given threshold, say 3%, to get the clusters? It’s not obvious to me how one should do this, or whether the answer is unique or depends on the cutting strategy. Is there a ‘standard’ method for doing this in the field?

Hi Robert,

We start with the smallest distance in the matrix and merge sequence/OTUs into new OTUs. When the smallest remaining distance goes over the threshold, we back it up a notch and use those assignments for the threshold. In the even that there are ties for the smallest distance we break the tie randomly and proceed. So the answer is not necessarily unique, but we do not find that there is a lot of run-to-run variation.