I'm comparing 12 Metagenomes. I'm using HMM counts of a number of proteins known to exists as groups within certain operons. I have grouped the HMM counts for each type of operon and calculated the Shannon-Weaver index for each Metagenome.
My question is: Can I compare these Indices? Is there a better test to use than Mann Whitney U test? I would like to do this on the ungrouped data, but I have many zeroes for some fields?