EIGENSTRAT in HelixTree

The technique implemented in HelixTree to correct input data for population stratification by principal component analysis is based on the  program EIGENSTRAT with a few enhancements. This technique was pioneered at the Broad Institute. The PCA correction technique is described in [Price 2006]. A more thorough discussion of stratification, principal components analysis, and the eigenvalues involved may be found in [Patterson 2006].

See the following chapter in the HelixTree manual for more information about how EIGENSTRAT and population stratification work within HelixTree.
http://www.goldenhelix.com/SNP_Variation/Manual/correction_for_stratification.html