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STRAT version 1.1

The program STRAT is a companion program to structure. It is written 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 (67:170-181). [Abstract][Manuscript]. See also Am. J. Hum Genet (65: 220-228) [Abstract], [Manuscript], [Review of structured association methods]


We ask that you fill out a web form to register software downloads.  Executables are currently available for the following platforms.

For UNIX: [Sun], and [Linux]. These are compressed in zip files; uncompress them using "unzip [filename]". 

For DOS/Windows: [DOS/Windows]. Brief notes on installation are here


In order to use STRAT, you should also download the structure software and place this in the same directory. 

Further details

The zip files contain an executable and parameter files, as well as a sample data file "testdata1". The program is set up to run on these data immediately (just type "./structure" and then "./STRAT" to run the programs). Documentation is included in the zip files, but can be downloaded directly from [here]

Bug in version 1.01 

Version 1.1 corrects a serious bug  that was introduced into STRAT version 1.01 (September 2002).   In the situations where this bug arose, it produced nonsensical output: massive chi-square values and undefined values of the test statistic.

Version 1.1 also introduces a number of minor updates to improve user-friendliness, described in the updated manual.

Comments, queries, or bug reports regarding any of these software should be directed to us at structure_help@genetics.uchicago.edu

Thank you!