More current research and software can be found at the eScience FaST-LMM site.
FaST-LMM (Factored SpectrallyTransformed Linear MixedModels) is a program for performing genome-wide association studies (GWAS) on large data sets. It runs on both Windows and Linux system, and has been tested on data sets with over 120,000 individuals [1,2].
- J. Listgarten*, C. Lippert*, C.M. Kadie, R.I. Davidson, E. Eskin, and D. Heckerman*.Improved linear mixed models for genome-wide association studies.Nature Methods, 9: 525-526, June 2012 (doi:10.1038/nmeth.2037). (*equal contributions)
- C. Lippert*, J. Listgarten*, Y. Liu, C.M. Kadie, R.I. Davidson, and D. Heckerman*. FaST linear mixed models for genome-wide association studies.Nature Methods, 8: 833-835, Oct 2011 (doi:10.1038/nmeth.1681). (*equal contributions)
Newer papers with improved algorithms can be found on the MSR eScience site for FaST-LMM.
Releases
Please go to the MSR eScience site for FaST-LMM for newer releases.
2012/05 - Future updates are now hosted on the MSR eScience site for FaST-LMM.
2012/04/06 - v1.09 - Several usability enahancements (MaxThreads), update to latest MKL libs (v10.3.7),
and misc fixes
2012/03/17 - v1.08 - Improve perf of SNC detection, add -extractSimTopK option, doc updates,
-verboseOut fixes
2012/03/06 - v1.07 - Fix bug 17541 -sim option not processing the alternate phenotype file properly
2012/02/27 - v1.06 - Detection and filtering of constant genotypes in a SNP
+ Bug fixes for binary and transposed files
2012/02/02 - v1.05 - Bug fixes
2012/01/05 - v1.04 - Add support for using dosage information + bug fixes
2011/11/21 - v1.03 - Add several perf enhancements relating -extract and -numjobs for improved
throughput and reduce memory usage
2011/09/27 - v1.02 - Add several perf enhancements relating to C++ for improved throughput and
reduce memory usage
2011/09/14 - v1.01 - Add -extract support to C# and small clean-up changes
2011/09/04 - v1.00 - Initial Release