cluster and cutoffs


This is a very basic question, I think, but I’m new with Mothur. I have Sanger generated data for a functional gene and produced an alignment in fasta format, created the phylip distance matrix (column formatted) using the dist.seqs command, as follows:

dist.seqs(fasta=aligned.fas, output=squared)

then I clustered using the cluster command, as follows:

cluster(phylip=aligned.square.dist, cutoff=0.05)

Hence, the list file should give me a list of the existing OTU’s at different levels, but I only get those that are unique, 0.01, 0.02 and 0.05… and I’d like have information regarding the 0.03 cutoff, because I want to compare the clusters I get with a 0.02 and 0.03 cutoff (98% and 97% respectively).

I’ve tried to set the cutoff to 0.04, 0.03, I’ve played with the “hard=t” and the “precision” options, and I still can’t figure this out… can someone help me with this, please?

Check this out…

Ok, now I feel pretty dumb, and the worst thing is that I actually checked the FAQ page. But anyway, thank you so much for pointing it out :smiley: