Haploview is a commonly used bioinformatics

Bioinformatics

Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...

 software which is designed to analyze and visualize patterns of linkage disequilibrium

Linkage disequilibrium

In population genetics, linkage disequilibrium is the non-random association of alleles at two or more loci, not necessarily on the same chromosome. It is also referred to as to as gametic phase disequilibrium , or simply gametic disequilibrium...

 (LD) in genetic

Genetics

Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....

 data. Haploview can also perform association studies, choosing tagSNPs and estimating haplotype

Haplotype

A haplotype in genetics is a combination of alleles at adjacent locations on the chromosome that are transmitted together...

 frequencies

Frequency

Frequency is the number of occurrences of a repeating event per unit time. It is also referred to as temporal frequency.The period is the duration of one cycle in a repeating event, so the period is the reciprocal of the frequency...

. Haploview is developed and maintained by Dr. Mark Daly's lab at the MIT

Massachusetts Institute of Technology

The Massachusetts Institute of Technology is a private research university located in Cambridge, Massachusetts. MIT has five schools and one college, containing a total of 32 academic departments, with a strong emphasis on scientific and technological education and research.Founded in 1861 in...

/Harvard Broad Institute

Broad Institute

The Broad Institute is a genomic medicine research center located in Cambridge, Massachusetts, United States. Although it is independently governed and supported as a 501 nonprofit research organization, the institute is formally affiliated with the Massachusetts Institute of Technology, Harvard...

.

Haploview currently supports the following functionalities:

• LD & haplotype block analysis
• Haplotype population frequency estimation
• Single SNP and haplotype association tests
• Permutation
  Permutation
  In mathematics, the notion of permutation is used with several slightly different meanings, all related to the act of permuting objects or values. Informally, a permutation of a set of objects is an arrangement of those objects into a particular order...
  
   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