What does cutoff mean with cluster(method=average, ...)

I have a quick question about the average neighbor clustering. Since it takes a long time, I thought I’d ask before trying it out: What does the “cutoff” option mean if clustering by average neighbor using the cluster() function? Is the cutoff applied to the distances as they are processed (i.e., the maximum distance considered is cutoff), or is it applied as the maximum cluster size reported in the output file?


should be the maximum cluster size reported; however, if you use cutoff on dist.seqs or read.dist, you may not get clusters all the way to your desired cutoff because average neighbor may be looking for distances beyond the cutoff. if this happens, cluster resets the cutoff to incorporate what it can see.