Eigenstrat

"The EIGENSOFTpackage combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model 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 EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes."

Project website: http://genepath.med.harvard.edu/~reich/Software.htm

Load SGE module
The following Modules file should be loaded for this package: module load eigenstrat/eigenstrat