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