EIGENSTRAT (Price et al. 2006) detects and corrects for population stratification in genome-wide association studies. The method, based on principal components analysis, explicitly models ancestry differences between cases and controls along continuous axes of variation. The resulting correction is specific to a candidate marker's variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The approach is powerful as well as fast, and can easily be applied to disease studies with hundreds of thousands of markers.

As of December 2006, EIGENSTRAT is implemented as part of the EIGENSOFT package. Source code, documentation and executables for the EIGENSOFT package are available at the Reich lab software page.