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structure

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 microsatellites, RFLPs and SNPs. This method was described in an article in Genetics 2000 (155: 945-959). [Abstract], [Manuscript], [Example]. ["Time-lapse" plots]

[Download Structure v 1.0]

[Download beta release of Structure v 2.0  (with graphical front end)]

Plotting program (by Noah Rosenberg) and data used for "Genetic Structure of Human Populations" (Science Dec 2002).


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). [Abstract], [Manuscript], [Review of structured association methods]

[Download software]

Note: in July 2002 we were alerted to a bug in the chi-square calculation for this program.  This has now been corrected.


Simulation programs

Download the simulation programs used for my 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 me at pritch@genetics.uchicago.edu.