GENEHUNTER-TWOLOCUS
The optimized and parallelized version GENEHUNTER-TWOLOCUS PARALLEL, as described by Dietter et al. ("Efficient two-trait-locus linkage analysis through program optimization and parallelization: application to hypercholesterolemia", European Journal of Human Genetics 12:542-550, 2004), can analyze larger pedigrees than the previous version. In particular, the optimization of the serial program, before parallelization, has resulted in a speed-up of a factor of more than 10. Therefore, using the new GENEHUNTER-TWOLOCUS PARALLEL version is already of benefit in the context of a computer with a single processor. The parallelization further decreases the computation time by a factor of the number of processors (i.e., perfect or linear speed-up). In addition, with this new version, the genetic positions of both trait loci are varied on their respective marker maps, not just the position of the second trait locus with the first one fixed, as before. The two-locus LOD and NPL scores are conveniently prepared to be displayed in three-dimensional plots, e.g. using Gnuplot or any other graphics package. Here is an example of such a plot, showing a two-locus LOD score of 4.44 that has been obtained in a linkage study of high factor VIII levels in venous thromboembolism (Berger et al., "High factor VIII levels in venous thromboembolism show linkage to imprinted loci on chromosomes 5 and 11", Blood 105:638-644, 2005).

Reference publications for GENEHUNTER-TWOLOCUS:
- Dietter J, Spiegel A, an Mey D, Pflug HJ, Al-Kateb H, Hoffmann K, Wienker TF, Strauch K (2004): Efficient two-trait-locus linkage analysis through program optimization and parallelization: application to hypercholesterolemia. European Journal of Human Genetics 12:542-550
- Strauch K, Fimmers R, Kurz T, Deichmann KA, Wienker TF, Baur MP (2000): Parametric and nonparametric multipoint linkage analysis with imprinting and two-locus-trait models: application to mite sensitization. American Journal of Human Genetics 66:1945-1957
Original GENEHUNTER references:
- Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES (1996): Parametric and nonparametric linkage analysis: a unified multipoint approach. American Journal of Human Genetics 58:1347-1363
- Kruglyak L, Lander ES (1998): Faster multipoint linkage analysis using Fourier transforms. Journal of Computational Biology 5:1-7
- Markianos K, Daly MJ, Kruglyak L (2001): Efficient multipoint linkage analysis through reduction of inheritance space. American Journal of Human Genetics 68:963-977