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
thanks Josh. Those papers do look informative. The main issue with my dataset is that it is not a random sample. It may not be feasible...
I have been having the same issue, but have tired to supplement my dataset with public data to try to solve this. It might be a problem with the lack of viral sequences from the environment? Some of the above reviews address how to capture more viral diversity. Best of luck.