Question

Software for Mcdonald-Kreitman test

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10.5 years ago

RB ▴ 20

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 • 6.1k views

ADD COMMENT • link updated 7.0 years ago by mt1022 ▴ 310 • written 10.5 years ago by RB ▴ 20

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DnaSP is the tool for running various test including MKT http://www.ub.edu/dnasp/DnaSP_OS.html. Hope this will help someone.

ADD REPLY • link 10.5 years ago by RB ▴ 20

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What have you tried? Here is MKT online.

ADD REPLY • link 10.5 years ago by PoGibas 5.1k

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hi Pgibas, Does any standalone tool exists for this?

ADD REPLY • link 10.5 years ago by RB ▴ 20

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What format is your data in?

ADD REPLY • link updated 4.9 years ago by Ram 44k • written 10.5 years ago by Zev.Kronenberg 12k

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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.

ADD REPLY • link updated 4.9 years ago by Ram 44k • written 10.5 years ago by RB ▴ 20

score 1 · Answer 1 · 2017-12-12

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).