Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. 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
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