I just new user in Mothur. I got the problem in my result to analyse 30,000 reads among 30 different samples which contains different number of sequences. I had create an alignment, create the distance matrix and phylogenetic tree in large file. After that I analysed in OTU with cluster command, but here I got only unique result. I understand that the distance was clustered follow the distance matrix which I run in Phylip, so I checked it back which was found that it has distance in 0.01, 0.03 or 0.05. I’m not sure what is the problem.
Thank you very much