As RDP reference files have many poor quality sequences, why SOP and other analyses used RDP reference files in classify.seqs? Can Silva seed database be used in classify.seqs?
I think that all of the databases have an equal number of poor sequences in them. They all do just about as good as each other when doing a leave one out testing scheme. They also vary in how well they classify samples from different environments. The nice thing about mothur is that you can use any of the classification databases that you might want to use. Go for it!