Hello.
I wonder what kind of algorithm does Mothur use to generate the distance matrix, using the dist.seqs() command? Is it the least square method? Just guessing…
What is more, I wander what the method of Clearcut() of yielding the phylogenetic tree?
Thank you very much!
By default, dist.seqs uses the one-gap distance calculation described at http://www.mothur.org/wiki/Dist.seqs. We also provide an ignore-gap and each-gap calculator within dist.seqs.
Depending on how you run clearcut it either does a relaxed-neighbor joining or a “real” neighbor joining. You’d have to check the original publications out of the U of Idaho for more details. We just wrap it and put a shiny label on it 
Thank you, Sir Pschloss.