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Structure 2.2

The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPs, microsatellites, RFLPs and AFLPs. The basic algorithm was described by Pritchard, Stephens & Donnelly (2000). Extensions to the method were published by Falush, Stephens and Pritchard (2003) and (2007).

Structure Homepage

STRAT

The program STRAT is a companion program to structure. This is a structured association method, for use in association mapping, enabling valid case-control studies even in the presence of population structure. This method was described in an article in Am. J. Hum Genet 2000 (67:170-181). Collaborators: Matthew Stephens, Noah Rosenberg, Peter Donnelly. [Abstract], [Manuscript], [Review of structured association methods].

[Download software].

SelSimStanding

A program to simulation population genetic data from a model of a selective sweep on standing variation (Przeworski, Coop and Wall Evolution 2005). The program will be available shortly. For further information please contact Graham Coop ( gcoop at bsd.uchicago.edu )

TreeLD 1.0

The package TreeLD is a free software tool for mapping complex trait loci. TreeLD performs a multipoint LD-analysis by inferring the ancestry of a genomic region and analyzing this ancestry for signals of disease mutations. The generated likelihoods can be used to test for the presence of a disease locus and to fine-map its location, providing a point estimate and a credible region. Furthermore, the package provides a novel way of visualizing the association signal in a sample. TreeLD is designed for high-density SNP haplotypes and can be applied to case-control data, TDT trio data and quantitative trait data.

The methods in this program are detailed in Zollner and Pritchard (2005).

Download TreeLD 1.0

MALDSoft

MALDSoft is a program for admixture mapping of complex trait loci, using case-control data. The samples should come from a recently-admixed; population; additional 'learning' samples from the parental populations are helpful. The method was described in a paper by Giovanni Montana and Jonathan Pritchard [Abstract] [Manuscript].

Download MALDSoft

Simulation programs

Download the simulation programs used for Pritchard's July 2001 AJHG article. One program is an implementation of the ancestral selection graph (for simulating genealogies with selection). The other program simulates a multi-locus model of complex disease.

Please report any problems to structure_help@bsd.uchicago.edu.