imbie famhap uni

Software from IMBIE
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FAMHAP is a software for single-marker analysis and, in particular, joint analysis of unphased genotype data from tightly linked markers (haplotype analysis). Some important features:

  • Analysis of case-control data and analysis of nuclear family data
  • Optimized for the haplotype frequency estimation of many markers
  • Provides LD measures and selects tagging markers
  • Searches for potential genotyping errors using haplotypes
  • Provides several methods for haplotype association analysis
  • Emphasis is on Monte-Carlo simulations and the issue of multiple testing
  • Case-control data: testing strategies for the simultaneous analysis of unlinked genomic regions
  • Nuclear family data: tests for association and imprinting
  • The latest FAMHAP version (released 08/2008) provides methods for the analysis of GWAS, imputation of genotypes and diplotype analysis
  • The additional program runFamhap allows to run the same kind of analysis repeatedly for varying marker sets, i.e. for application to GWAS
  • A graphical user interface is now available that facilitates the usage of the program


Becker T, Knapp M (2004) Maximum-Likelihood Estimation of Haplotype Frequencies in Nuclear Families. Genet Epidemiol 27: 21-32

Herold C, Becker T (2009) Genetic association analysis with FAMHAP: a major program update. Bioinformatics 1;25(1):134-6