* [[http://www.r-project.org/|R]]
    * [[http://openmx.psyc.virginia.edu/|OpenMx]]
    * [[http://cran.r-project.org/web/packages/corpcor/|corpcor]]
    * [[http://cran.r-project.org/web/packages/MASS/|MASS]]
    * [[http://cran.r-project.org/web/packages/psych/|psych]]
    * [[http://cran.r-project.org/web/packages/mvtnorm/|mvtnorm]]
  * [[http://www.sph.umich.edu/csg/abecasis/Merlin/|Merlin]]
  * [[http://www.sph.umich.edu/csg/abecasis/MACH/|MACH]]
  * [[http://www.sph.umich.edu/csg/abecasis/Metal/index.html|Metal]]
  * [[http://genome.sph.umich.edu/wiki/Minimac|Minimac]]
  * [[http://pngu.mgh.harvard.edu/~purcell/plink/|plink]]
  * [[http://www.vcu.edu/mx/|Old Mx]]
  * [[http://gump.qimr.edu.au/VEGAS/|VEGAS]]
  * [[https://groups.google.com/group/quantisnp?hl=en|QuantiSNPv2]]