Analysis tool for replicated data (ANOSIM OR AMOVA)

We’re getting to the point where the sequencing of replicates is looking more and more feasible. I’d like to see an analysis of similarity (ANOSIM), MANOVA, or AMOVA-type module built in to Mothur. It should be a fairly simple step (she says naively) beyond building list file. The way that I’m envisioning the work flow would be:

  1. (…and the steps leading up to it) delineating OTUs over a data set that comprises replicated sequence libraries over multiple experimental treatments/conditions
  2. As we do already, a a groups file would need to be provided, but in addition, we would also need to provide a file that defines how the libraries fit into the replication “scheme”
  3. The list file would need to be formatted as a matrix of samples vs OTU counts (or relative abundances)
  4. Calculation of the F statistic (at all distance levels or at a user-specified distance level)