PDF)Genehunter 2 is an extension of the GENEHUNTER software. It can perform multipoint LOD scores, non-parametric linkage statistics, and now in a wide range of sibpair analyses (as in MAPMAKER/SIBS) and a new variance components analysis. In addition, several TDT analyses are also available for searching for association/disequlibrium in addition to linkage. Genehunter can analyze pedigrees of moderate size only.
L. Kruglyak, M.J. Daly, M.P. Reeve-Daly, and E.S. Lander. "Parametric and Nonparametric Linkage Analysis: A Unified Multipoint Approach". American Journal of Human Genetics 58:1347-1363 (June 1996).
L. Kruglyak and E.S. Lander. "Faster Multipoint Linkage Analysis Using Fourier Transforms". Journal of Computational Biology 5:1-7 (1998).
Genehunter v. 2.1_r4 beta documentation (PDF)