Haploview is a commonly used
bioinformatics software The list of bioinformatics software tools can be split up according to the license used:
* List of proprietary bioinformatics software
* List of open-source bioinformatics software
Alternatively, here is a categorization according to the respective ...
which is designed to analyze and visualize patterns of
linkage disequilibrium
In population genetics, linkage disequilibrium (LD) is the non-random association of alleles at different loci in a given population. Loci are said to be in linkage disequilibrium when the frequency of association of their different alleles is h ...
(LD) in
genetic data. Haploview can also perform association studies, choosing tag
SNPs
In genetics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in a sufficiently larg ...
[{{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
The Massachusetts Institute of Technology (MIT) is a private land-grant research university in Cambridge, Massachusetts. Established in 1861, MIT has played a key role in the development of modern technology and science, and is one of the m ...
/
Harvard Broad Institute
The Eli and Edythe L. Broad Institute of MIT and Harvard (IPA: , pronunciation respelling: ), often referred to as the Broad Institute, is a biomedical and genomic research center located in Cambridge, Massachusetts, United States. The institu ...
.
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
In computer networks, download means to ''receive'' data from a remote system, typically a server such as a web server, an FTP server, an email server, or other similar system. This contrasts with uploading, where data is ''sent to'' a remote ...
of phased genotype data from
HapMap
The International HapMap Project was an organization that aimed to develop a haplotype map (HapMap) of the human genome, to describe the common patterns of human genetic variation. HapMap is used to find genetic variants affecting health, disease a ...
* Visualization and plotting of PLINK whole genome association results including advanced filtering options
References
External links
Haploview Homepage
Genetics software