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Interpreting STRUCTURE/ADMIXTURE using badMIXTURE and mixPainter

badMIXTURE is an R Package for describing whether a mixture model (as produced by e.g. ADMIXTURE or STRUCTURE) is safe to interpret as-is, or whether the residuals indicate that the interpretation shouldn't be taken literally.

mixPainter is a piece of software to simply use Chromosome Painting for input into badMIXTURE.

badMIXTUREexample shows exactly how we processed the data in the paper, starting from PLINK format data.

ADMIXTURE and STRUCTURE are amongst the most popular tools in population genetics. They, along with a large number of related tools, model populations as mixtures of ancestral populations. These results can sometimes be misleading, if the ancestral populations in the model never existed in history.

Link to the paper

See A tutorial on how (not) to over-interpret STRUCTURE/ADMIXTURE bar plots, by Daniel Falush, Lucy Van-Dorp and Daniel J Lawson (2016 BioArxiv preprint).