I use the command “dist.seqs”, “read.otu” and “cluster” to get OTUs. And the bin.seqs command to get the OTUs sequences. However I found that the sequences in an OTU are not consistent with the parameters I want.
For example I set the cutoff=0.03, however, I found there are sequences with different length in one OTU; One of the sequences in the OTU is 60bp, while the others are 53bp. Is that the bug of MOTHUR, or I just misunderstood the construction of distance matrix? Thank you~