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Resource Name
Haploview
RRID:SCR_003076 RRID Copied      
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Haploview (RRID:SCR_003076)
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Resource Information

URL: http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview

Proper Citation: Haploview (RRID:SCR_003076)

Description: A Java based software tool designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently allows users to examine block structures, generate haplotypes in these blocks, run association tests, and save the data in a number of formats. All functionalities are highly customizable. (entry from Genetic Analysis Software) * 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 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. Note: Haploview is currently on a development and support freeze. The team is currently looking at a variety of options in order to provide support for the software. Haploview is an open source project hosted by SourceForge. The source can be downloaded at the SourceForge project site.

Abbreviations: Haploview

Resource Type: data processing software, source code, software resource, software application

Defining Citation: PMID:15297300, PMID:21356869, PMID:20147036

Keywords: linkage disequilibrium, haplotype, genotype, visualization, analysis, single nucleotide polymorphism, gene, genetic, genomic, java

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This resource

is listed by

Genetic Analysis Software

is listed by

SoftCite

is related to

International HapMap Project

is related to

PLINK

has parent organization

Broad Institute

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