how to do a MK test analysis
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2.2 years ago
Kay ▴ 10

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.


McDonald-Kreitman test MK test Paml • 748 views
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It may be a good idea to contact the developers. This program is not commonly used.


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