Haploview[1] is a commonly used bioinformatics software which is designed to analyze and visualize patterns of linkage disequilibrium (LD) in genetic data.
Haploview can also perform association studies, choosing tagSNPs[2] and estimating haplotype frequencies.
Haploview is developed and maintained by Dr. Mark Daly's lab at the MIT/Harvard Broad Institute.
Haploview currently supports the following functionalities: