HAPLOCLUSTERS is a program designed to detect excess haplotypes sharing in datasets consisting of case and control haplotypes. Excess haplotype sharing can be seen around disease loci in case samples since LD persists longer here than in the controls where LD is persisting only according to the relatedness of the individuals in the population, i.e. the age of the population. This LD is often referred to as background LD.
Melanie Bahlo (firstname.lastname@example.org) @ WEHI Bioinformatics
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Bahlo M, Stankovich J, Speed TP, Rubio JP, Burfoot RK, Foote SJ.
Detecting genome wide haplotype sharing using SNP or microsatellite haplotype data.
Hum Genet. 2006 Mar;119(1-2):38-50.