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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.

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    $\begingroup$ Are you asking "What are the definitions of these three statistics?" or "What software can I use to compute these three statistics?". If your question is about a software, you should definitely specify how formatted your data are (VCF, FASTA , GENEPOP, SAM, etc...?) $\endgroup$ – Remi.b May 21 at 15:45

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