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Beagle
BEAGLE is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. This software is not installed system-wide, as it does not require such. Instead download it by using the following: wget http://www.stat.auckland.ac.nz/~bbrowning/beagle/beagle.jar
R
In addition, many genetics R based software packages are installed. See above R listing.