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
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 is being maintained at the Alkes Price lab software page and 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
HAPMIX (Price et al. 2009) uses genotyping data from SNP arrays to infer chromosomal segments of distinct continental ancestry in admixed populations. Source code is being maintained on the Alkes Price lab website 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. Please contact Hua Chen if you have questions about the software.

ADMIXTOOLS 1.1 (February 2013)
ADMIXTOOLS (Patterson et al. 2012) is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates. It can be downloaded for LINUX (see documentation). The software package also includes Affymetrix Human Origins Curated Dataset. Write to Arti Tandon if you have questions about the software and for scientific questions write to Nick Patterson. The new release fixes a serious bug in qpDstat.

HAPI-UR 1.0 (September 2012)
HAPI-UR (Williams et al. 2012) is a program for inferring phased haplotypes from unphased genotypes. Please see the HAPI-UR software website to download the software, including source code and documentation. Write to Amy Williams if you have questions about the software or scientific questions.

ALDER 1.0 (November 2012)                                                                                                   ALDER (Loh, Lipson et al. 2013) is a software package that computes weighted linkage disequilibrium (LD) curves, which can be used to infer admixture parameters including dates, mixture proportions, and phylogeny. This package extends the methodology of the ROLLOFF software in ADMIXTOOLS. Source code and documentation can be downloaded here. Write to Po-Ru Loh or Mark Lipson if you have questions.

MixMapper 1.0 (December 2012)                                                                                MixMapper (Lipson, Loh et al. 2012) is a software package that analyzes allele frequency correlations among multiple populations simultaneously to build a tree (or “admixture graph”) of population relationships that incorporates the possibility of mixture. This package complements ADMIXTOOLS, with the key difference that it semi-automatically searches the space of possible admixture graph topologies to find the best fit for the data. Source code and documentation can be downloaded here. Write to Mark Lipson or Po-Ru Loh if you have 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.