hapQTL: haplotype Quantitative Loci
This software performs association testing between local haplotypes and phenotypes at each core marker. It doesn't require phasing or an arbitrary window to specify haplotypes. It is the companion software for the paper Xu and Guan (2014).
ELAI: Efficient Local Ancestry Inference
The software performs local ancestry inference for two-way, three-way, or multi-way admixed individuals. It is the companion software for the paper Guan (2014).
piMASS: Posterior Inference via Model Averaging and Subset Selection
The software performs multi-SNP association with disease phenotypes, and it can handle all SNPs in the genome simultaneously. It is the companion software for the paper Guan and Stephens (2011).
BIMBAM: Bayesian Imputation Based Association Mapping
The software performs genotype imputation and statistical tests for disease association, including single SNP tests and regional multi-SNP tests
WinSSS: Windows-based Stochastic Spatial Simulator
This is a Windows-based software. It implements many classical models in interacting particle systems, for example, the multiple contact process, the Greenberg Hastings process, and the generalized Rock-Scissor-Paper dynamic. The real time animations are rendered by OpenGL.