HAPSTAT is a user-friendly software interface for the statistical analysis of haplotype-disease association. HAPSTAT allows the user to estimate or test haplotype effects and haplotype-environment interactions by maximizing the (observed-data) likelihood that properly accounts for phase uncertainty and study design. Cross-sectional, longitudinal, case-control and cohort studies are considered. The underlying methodology and a subset of the numerical algorithms used in HAPSTAT are found in Lin and Zeng (JASA, 2006), Lin, Zeng and Millikan (Genetic Epidemiology, 2005), Zeng, Lin, Avery, North and Bray (Biostatistics, 2006) and Lin, Hu and Huang (American Journal of Human Genetics, 2008). The current version allows haplotype analysis of multiple genes as well as single- and multi-SNP analysis with missing genotypes, as as described in Lin, Hu and Huang.

The latest software release is HAPSTAT 3.0. The current and previous versions of the HAPSTAT software are available from the download page. As this software and related materials are still under development, please check back frequently for updates.

Your comments are welcome! If you encounter problems using HAPSTAT, have questions or suggestions for improvement, please contact us at linsoft@bios.unc.edu.