The output of the PLINK and ADMIXTURE algorithms we are going to present here, is supposed to reflect "genetic substructures" in both subsample of project participants and reference populations. I guess that the best practice for analyzing admixture would be to dissect populations, starting with K=3 or K=4 assumed explicit ancestral populations and ascending to K=7 or K=8 (although the latter K is a doubtless overkill, and that can lead to the formation of "spurious" clusters).

I used Razib Khan's script to visualize the output of Admixture run for MDL sample (please don't read too much into the first experimental results, because i disclaim all liability for harm done by the inaccurate misinterpretation of results :) ).

MDS plot of genetic distances between populations on the basis of ~500 000 snps

MDS GNUplot (read Davidski's post explaining how datasheets (read: Plink matrix files*) that can be turned into interactive genetic maps with just a couple of simple commands in GNUplot). In Plink, to perform multidimensional scaling analysis on the N x N matrix of genome-wide IBS pairwise distances, use the --mds-plot option in conjunction with --cluster. This command takes a single parameter, the number of dimensions to be extracted. For example, assuming we have already calculated the plink.genome file,

plink --file mydata --read-genome plink.genome --cluster --mds-plot 4

creates the file

     plink.mds

I hadn't enough time to find informative angles, so please take a look at plot as it is. The legend of plot is the same as in previous posts.

The same MDS plot with population ID labels