Razib Khan One-stop-shopping for all of my content

July 27, 2011

DIY admixture analysis

Dienekes Pontikos has just released DIY Dodecad, a DIY admixture analysis program. You can download the files yourself. It runs on both Linux and Windows. Since I already have tools in Linux I decided to try out the Windows version, and it seems to work fine. It is somewhat limited in that you start out with the parameters which Dienekes has set for you, but if you don’t want to write your own scripts and get familiar with all the scientific programs out there, I think this is a very good option. Additionally, it seems to run rather fast, so you won’t spend days experimenting with different parameters.

Dienekes has already run me, but I put my parents’ genotype files through the system. Here are the results:

Population Razib Mother Father East_European 6.9 6.5 4.3 West_European 1.7 3.1 5.5 Mediterranean 6.3 5.6 5.9 Neo_African 0 0 0 West_Asian 0 2 3.9 South_Asian 65.9 59.6 60.4 Northeast_Asian 2.9 3.8 3.6 Southeast_Asian 15.8 16.6 15.5 East_African 0 0 0.2 Southwest_Asian 0.5 2.5 0.7 Northwest_African 0 0 0 Palaeo_African 0 0.3 0

The main thing to notice is that my mother has more total East Asian ancestry than my father, and, that she has a Southwest Asian component which is at a few percent. These are always consistent findings in the dozens of ADMIXTURE runs I’ve done with various parameter settings and reference population mixes, so it’s nice that DIY Dodecad replicates those findings. Though the population sets seem a bit Eurocentric to ...

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