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.