HaploView

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 is fully compatible with data dumps from the HapMap project and the Perlegen Genotype Browser. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals.

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 and automatic download of phased genotype data from HapMap.
* visualization and plotting of PLINK whole genome association results including advanced filtering options