Have you seen the Leinster and Cobbold approach to measuring diversity? Any plan to implement in mothur?
Leinster T, Cobbold CA. 2012. Measuring diversity: the importance of species similarity. Ecology 93(3):477-489.
Thanks for the reference. We do have the phylogenetic diversity metric which does take into account sequence similarity. I should caution that this makes the assumption that sequence similarity is correlated with function, which might be a bit of a stretch. Of course, this doesn’t stop people from using it and getting Science papers ;).
Pat
There is a second angle to their proposal (besides incorporating ‘similarity’ into the diversity index), which is to look at ‘diversity profiles’ - i.e., a continuum of diversity indices which give progressively less weight to rare members of the community.
A couple of papers have explored how this might be helpful in relation to microbial sequence-based datasets specifically:
Doll 2013 BMC Microbiology http://www.biomedcentral.com/1471-2180/13/259
Veresoglou 2014 Fungal Ecology http://dx.doi.org/10.1016/j.funeco.2014.03.006