Have you tried split.abund (http://www.mothur.org/wiki/Split.abund)? We haven’t played with it much, but I think it could serve your needs. If it doesn’t just holler and we’ll try to make some improvements.
Pat
+1 vote for an option to exclude single-seq OTUs in some cases, we were just discussing the same need some days ago.
In what way would you define a singleton? For a single group, across a pair of groups, across all groups?