Aberrant is a R package for automatically indentiying outliers from otherwise Guassian distributions. It is designed for excluding samples from genome-wide association studies which have summary statistics of variation which differ from the sample at large.

Celine Bellenguez, Amy Strange, Colin Freeman, Wellcome Trust Case Control Consortium 2, Peter J Donnelly and Chris CA Spencer. (2011) A robust clustering algorithm for identifying problematic samples in genome-wide association studies. Bioinformatics. 2012 Jan 1;28(1):134-5.

 Download R package: Aberrant_1.0.tar.gz manual: Aberrant-manual.pdf 

GWApower is a R package for assessing the power of genome-wide association studies using commercially available genotyping chips. The package encapsulates extensive simulation results generated by the program HAPGEN.
Spencer, C., Su, Z., Donnelly, P. and Marchini, J. Designing Genome-Wide Association Studies: sample size, power, and the choice of genotyping chip. PLoS Genet. 2009 May;5(5):e1000477.

Download R package: GWApower_1.1.tar.gz

SelSim is a command line program for simulating data from the coalescent with recombination and a single locus under natural selection. Both stochastic and deterministic models of selection are available. The program is no longer supported.

Spencer C., Coop, G. (2005) SelSim: a program to simulate population genetic data with natural selection and recombination. Bioinformatics. 2004 Dec 12;20(18):3673-5.

Website : SelSim