HaploView is a tool to analyze and visualize LD haplotype maps. The HaploView includes functions for LD and haplotype block analysis, population frequency estimation, single SNP and haplotype association tests, permutation testing, Paul de Bakker's Tagger tag SNP selection algorithm, download of phased genotype data from HapMap, visualization, and plotting.
Barrett JC, Fry B, Maller J, Daly MJ "Haploview: analysis and visualization of LD and haplotype maps." Bioinformatics. 2005 Jan 15;21(2):263-5. 2004 Aug 5. https://doi.org/10.1093/bioinformatics/bth457
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