CCREL (Case-Control association analysis with RELlated individuals) is a program for case-control genetic analysis that takes relatedness between individuals into account. It will perform single-marker and haplotypic tests, however it will only work with SNP or other biallelic markers.
:: MORE INFORMATION
Browning, Briley, Briley, Chandra, Charnecki, Ehm, Johansson, Jones, Karter, Yarnall, Wagner (2005),
“Case-control single marker and haplotypic association analysis of pedigree data“,
Genetic Epidemiology, 28:110-122.