Hi boys and girls,
I am writing a review about the evolution of a specific virus family. I though it would be informative to try to estimate the diversity within this family of viruses. To date the community has isolated ~250 unique viral types. A unique type is defined as having <90% sequence identity across a certain ORF.
Does anyone know of any tools (I though about rarefaction curves) I could use to estimate the diversity? Calculating the effective population size may be a possibility? However, it requires one to know (or estimate) the viral evolutionary rate.
Any help would be greatly appreciated