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). Write to Arti Tandon if you have questions about the software and for scientific questions write to Nick Patterson.

EIGENSOFT 5.0
(August 2013) EIGENSOFT version 5.0.1 is now available for download. The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction 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.

Source code, documentation, and executables for using EIGENSOFT 5.0 on a Linux platform are maintained on the Alkes Price lab website and can be downloaded here. New features of EIGENSOFT 5.0 include expanded options for LD regression in computing the GRM, a new option for PCA projection with large amounts of missing data, and a bug fix for PLINK format files with out-of-order SNPs. EIG5.0.1 incorporates a minor bug fix in the GRM input routines. However, EIGENSOFT 5.0 does not support multi-threading. Users who wish to use multi-threading should use EIGENSOFT 4.2, which can be downloaded on the Alkes Price lab website here.

The EIGENSOFT FAQ is available here. For further questions about the EIGENSOFT software, please write to Samuela Pollack.

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.