Question: how to do a MK test analysis
gravatar for Kay
23 months ago by
Liverpool, UK
Kay10 wrote:

Hi everyone, I'm trying to use MK test version 2.0

But I don't quite understand the data input structure. It's asking for Dn and Ds (Integer-valued counts of between-species divergence for non-synonymous and synonymous substitutions), I understand yn00 from PAML might help with that, Pn and Ps (Integer-valued counts of within-species polymorphism for non-synonymous and synonymous mutants), If I am correct this I can get from VCF file from isolates within the specie of interest by counting the number of non-synonymous and synonymous within the specie for the gene of interested respectively. It also asks for Ln and Ls (the number of non-synonymous and synonymous sites in the gene)---- this I don't seem to understand.

The input data should look something like this (the last 3 are voluntary);

1 2 3 4 5 6 7 8 9 [10 11 12]
DN LN(D) PN LN(P) DS LS(D) PS LS(P) alleles Chr Class r

Has any used the tool before or could help me explain what Ln and Ls means, and how to get this.


ADD COMMENTlink written 23 months ago by Kay10

It may be a good idea to contact the developers. This program is not commonly used.

ADD REPLYlink written 23 months ago by Kevin Blighe69k
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