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