Software

ANCESTRYMAP 2.0
ANCESTRYMAP (Patterson et al. 2004) finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux (see tutorial and documentation (online / PDF). Write to Arti Tandon if you have questions about the software and for scientific questions write to Nick Patterson.

EIGENSOFT 4.2 (NEW! August 30, 2011) 
EIGENSOFT uses PCA to correct for population stratification in medical association studies (EIGENSTRAT, Price et al. 2006) and to detect and analyze population structure (SMARTPCA, Patterson et al. 2006). Source code, documentation and executables for Linux can be downloaded here. Write to Samuela Pollack if you have further queries about the software that are not addressed on the FAQ page. Write to Alkes Price or Nick Patterson with scientific questions.

HAPMIX 1.2 (March 14, 2011)
HAPMIX (Price et al. 2009) uses genotyping data from SNP arrays to infer chromosomal segments of distinct continental ancestry in admixed populations, and can be downloaded here. Write to Simon Myers if you have scientific questions and to Arti Tandon if you have questions about the software.

XP-CLR 1.0
XP-CLR (Chen et al. 2010) uses allele frequency differentiation at linked loci to detect selective sweeps. Source code and documentation can be downloaded here. Write to Hua Chen if you have scientific questions.

Registration
We encourage users of our software to register here.

Principal Component Analysis of data from                               HAPMIX analysis of a Mozabite north African shows      

Iceland using EIGENSOFT shows a ring-like                              long and short stretches of sub-Saharan African ancestry,   

population structure that recapitulates geography.                    reflecting admixture at different time scales.