Software

Please visit here to access Reich lab software through GitHub.


cTools
cTools (written by Nick Patterson, Mengyao Zhao; see Mallick et al. 2016) provides software tools for accessing Simons Genomic Diversity Project data without unzipping the compressed files.

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. 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.

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.

ADMIXTOOLS
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. Please contact Nick Patterson if you have any questions about the software and for scientific questions.
* The latest ADMIXTOOLS release is available at GitHub. *
* Download the example data set here.

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.

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.

EIGENSOFT
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.
* The latest EIGENSOFT(EIG) version is available here and on the Alkes Price lab website.
**The EIGENSOFT FAQ is available here. 
***Three looks at 'shrinkage' in PCA***

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 or MAC (see tutorial). Please write to Nick Patterson if you have any questions about the software and for scientific questions. 
* The ANCESTRYMAP Software Documentation is available here.

Registration
We encourage users of our software to register here.