Haploview

Haploview{{cite journal|author1=Barrett J.C. |author2=Fry B. |author3=Maller J. |author4=Daly M.J. |title=Haploview: analysis and visualization of LD and haplotype maps|journal=Bioinformatics|year=2005|volume=21|pages=263–5|doi=10.1093/bioinformatics/bth457|pmid=15297300|issue=2|doi-access=free}} 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{{cite journal|author1=de Bakker P. I. |author2=Yelensky R. |author3=Pe'er I. |author4=Gabriel S. B. |author5=Daly M. J. |author6=Altshuler D. |title=Efficiency and power in genetic association studies|journal=Nature Genetics|year=2005|volume=37|pages=1217–23|doi=10.1038/ng1669|pmid=16244653|issue=11}} 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