the use cluster()

I use the cluster(cutoff = 0.03) command to generate a list file. However, when the sequences are too little to get OTUs at the distances of 0.03, the 0.03 line will not exist. How can i generate the 0.03 distance no matter how many sequences are clustered ?

There’s no way to force it to output 0.03; however, if you are using mothur for your downstream analysis, you don’t have to worry about it. We programmed a mother’s intuition into mothur so it’ll use 0.02 for rarefaction curves, etc. if 0.03 is missing.