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Software for Mcdonald-Kreitman test

Dear All,

I am new to population-genetics area. Can anyone please let me know if the pop-gen community performs tests like Mcdonald-Kreitman, HKA by writing there own scripts or any software exists for these?

Thanks,

RT

population-genetics mcdonald-kreitman
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updated by mt1022 mt1022 • written by RB • RB

hi Pgibas, Does any standalone tool exists for this?

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written by RB • RB

What format is your data in?

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updated by Ram Ram • written by Zev.Kronenberg Zev.Kronenberg

My data is in fasta format. I have within species data for around 1000 individuals and I can't submit all that on MKT online server. That's why I am looking for a standalone tool.

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updated by Ram Ram • written by RB • RB

1 answer

Standard MK test is influenced by population demography and selective forces acting on nearby sites. Asymptotic estimate of alpha has been shown closer to real alpha based on simulations (Messer & Petrov 2013). There is also a web server to calculate asymptotic alpha (http://benhaller.com/messerlab/asymptoticMK.html) and the scripts can be downloaded from github and run within R (https://github.com/MesserLab/asymptoticMK/blob/master/asymptoticMK_local.R).

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written by mt1022 mt1022

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