I got different polymorphisms of Cucumber mosaic virus in different regions of its genome from different libraries of RNAseq.
This virus have two coding regions which are 3A and CP regions.
I have information of what polymorphism I have, in which site and the number of times that the reference and alternative nucleotide appear and total coverage.
I would like to know how to get the different diversity paramethers, such as Nei Diversity, Fst, Gst.
Thanks in advantage.