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Haploview
From Wikipedia, the free encyclopedia
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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
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