Record added by Jurg Ott (the original Rockefeller list)




FAMHAP is a tool for haplotype association analysis of unphased genotype data. It can be used both for population data (case-control) and nuclear family data. The program is optimized for haplotype frequency estimation with the EM-algorithm for many markers. FAMHAP provides a method which searches for potential genotyping errors and several tests for haplotype-based association analysis. Particular emphasis is on Monte-Carlo simulations, which are necessary in the context of haplotype association, where asymptotic theory often fails, and in the context of multiple testing problems.


  • Tim Becker (email: tim.becker@ukb.uni-bonn.de)

  • Michael Knapp






UNIX, MS-Windows, MacOS


  • Becker, Knapp (2004), “Maximum-likelihood estimation of haplotype frequencies in nuclear families”, Genetic Epidemiology, 27;21-32.

  • Becker, Knapp (2004), “A powerful strategy to account for multiple testing in the context of haplotype analysis”, American Journal of Human Genetics, 75:561-570

  • Becker, Knapp (2005), “Impact of missing genotype data on Monte-carlo simulation based haplotype analysis”, Human Heredity, 59:185-189.

  • Becker, Cichon, J├Ânson, Knapp (2005), “Multiple testing in the context of haplotype analysis revisited: application to case-control data”, Annals of Human Genetics, 69:1-10

  • Becker, Schumacher, Cichon, Baur, Knapp (2005), “Haplotype interaction analysis of unlinked regions”, Genetic Epidemiology, 29:313-322.

  • Becker, Valentonyte, Croucher, Strauch, Schreiber, Hampe, Knapp (2006), “Identification of probable genotyping errors by consideration of haplotypes”, European Journal of Human Genetics, 14:450-8.

  • Becker, Baur, Knapp (2006), “Detection of parent-of-origin effects using haplotype analysis”, Human Heredity, 62:64-76