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More current research and software can be found at the eScience FaST-LMM site:
http://research.microsoft.com/en-us/um/redmond/projects/MSCompBio/Fastlmm
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These files contain the files necessary to run FaSTLMM on Windows or Linux along with the license and users manual. To download FaSTLMM source code, please follow the changeset link located above to the Source Code tab.
The FaSTLMM.Win.zip download contains both C++ and CSharp executable versions of FaSTLMM. No installer is required, just UnZip the file into a directory and run from there. Or put the installation directory on your path and run it from anywhere. The C++ version included runs on the 64 bit OS version while the CSharp version runs on both 64 and 32 bit versions of the OS.
The FaSTLMM.Linux.zip download contains the C++ executable and has been run on the Ubuntu distribution.
NOTE: The Beta status does not indicate a low quality release. The Beta status does indicate there is ongoing active development with updates and new features being delivered frequently.
v1.09
This version contains several usability enhancements sent from users. This includes a 'pre-check' that the output file is writable to prevent a write failure at the end of a long run. It also includes support for -MaxThreads to control threading and CPU usage. This is in support of running multiple jobs in a cluster situation. We also updated the system to use the latest MKL libraries (v10.3.7) on both Windows and Linux. And we fixed some bugs where intersection of data across plink, alternate phenotype, and covariates files were improperly failing to produce output.
v1.08
This version contains significant performance improvements to SNC detection and reduce the memory requirements for processing binary files. In addition -verboseOut reports have been 'cleaned' up the doc has been updated to reflect the new output format and options.
v1.07
This version contains the fix for bug 17541 which was causing an error in -sim file operations. Individuals must be unique in the family name and individual name and the unique key is a concatenation of these two pieces of information with a space separator. The -sim file requires a <tab> to separate fields so FAM<sp>INDIVIDUAL is a valid input
V1.06
This version adds detection and filtering of constant genotypes in a SNP allong with bug fixes.
V1.05
This version primarily fixes problems in -extract C++ memory management and the C# dll references to Sho.
V1.04
This version now contains the much requested dosage data. See the updated manual for specific instructions. In addition, several fixes around file handling on Linux were incorporated in this drop.
V1.03
This version has several more improvements to throughput and memory reduction, especially when partioning the inputs with -numjobs or -extract and numerous bug fixes. (Linux version updated 12/12/2011 with small bug fix - see change list 83740)
V1.02
The C++ version has several improvements to throughput and memory reduction.
V1.01
The C# version now supports the -extract option and the documentation is updated.
In addition, these files contain some small clean-up changes from the 1.0 release
V1.0
Initial release