I have a question concerning the algorithm used to assign sequences to OTUs (Average neighbour). What do you think about differences (advantages/disadvantages) in comparison to the algorithm described by Edgar (2013)? Is it planned to implement this algorithm to Mothur?
Maybe the pre.cluster command applies some of the issues just before cluster.spilt (preference of high-abundant reads to form OTUs). But I am not sure.
Thanks Andreas
Edgar, R.C. (2013) UPARSE: Highly accurate OTU sequences from microbial amplicon reads, Nature Methods 10, 996–998

No, we’re pretty unlikely to incorporate the UPARSE method. It’s closed source and the methods are pretty poorly defined and justified in the paper. See here: