Just a little plug for a Mendeley reference collection I have been helping make on “Phylogenetic and related analyses of metagenomic data.” If you want to know more about such studies you can find a growing list of publications at they group collection. http://www.mendeley.com/groups/1152921/_/widget/29/10/
Phylogenetic and related analyses of metagenomic data is a group in Biological Sciences on Mendeley.