EIGENSOFT 6.0.1 – Population Structure , Eigenanalysis & Stratification



EIGENSOFT package 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.


Reich laboratory




  • Linux





Nature Genetics 38, 904 – 909 (2006) Published online: 23 July 2006; | doi:10.1038/ng1847
Principal components analysis corrects for stratification in genome-wide association studies
Alkes L Price, Nick J Patterson, Robert M Plenge, Michael E Weinblatt, Nancy A Shadick & David Reich

Population Structure and Eigenanalysis
Nick Patterson, Alkes L. Price, David Reich
December 2006 Issue of PLoS Genetics

Leave a Reply

Your email address will not be published. Required fields are marked *


This site uses Akismet to reduce spam. Learn how your comment data is processed.