HaploViewHaploView 
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HaploView (hapinstall.exe). This program is designed to simplify and expedite the process of haplotype analysis by providing...
Streamline basic and advanced molecular genetic testing while identifying DNA segments with shared similarities. Process data from the HapMap Project, PHASE, or PLINK, customize analysis parameters, and manage individual datasets or run everything in efficient batch mode. Ideal for high-throughput genome analysis workflows and researchers seeking the best genetic analysis software.
Haploview simplifies and accelerates haplotype analysis by offering a unified interface for multiple genomic tasks. Fully compatible with HapMap project data dumps and the Perlegen Genotype Browser, it handles thousands of SNPs—tens of thousands via command line—across large cohorts. Designed for molecular biology data processing, population studies, and advanced linkage mapping.
Core features include LD and haplotype block analysis, haplotype frequency estimation, single SNP and haplotype association tests, permutation-based significance testing, automated download of phased genotype data, and integration of Paul de Bakker's Tagger tag SNP selection algorithm. It also supports visualization and plotting of PLINK whole-genome association results with robust filtering options—perfect for comprehensive genomic research pipelines.