Haploview

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:

• LD & haplotype block analysis
• Haplotype population frequency estimation
• Single SNP and haplotype association tests
• Permutation testing for association significance
• Implementation of Paul de Bakker's Tagger tag SNP selection algorithm
• Automatic download of phased genotype data from HapMap
• Visualization and plotting of PLINK whole genome association results including advanced filtering options

The Snagger extension for Haploview can be used to select tag SNPs using pairwise r² linkage disequilibrium.