Chapter 4 - About Haploview

About Haploview

Haploview was developed at and is maintained by Mark Daly's lab at the Broad Institute by Jeffrey Barrett, Julian Maller, David Bender and Jesse Whitworth. Questions and comments should be addressed to:

  • The design of the LD and haplotype interfaces is the work of Ben Fry at the MIT Media Lab.
  • Thanks to Andrew Kirby and Hin-Tak Leung for code contributions.
  • Thanks to Itsik Pe'er and Paul de Bakker for their extensive contributions to methods development and testing.
  • Hardy-Weinberg calculation code courtesy of Goncalo Abecasis and Jan Wigginton at the University of Michigan Center for Statistical Genetics
  • The r2 and alternative D' color schemes are the work of Will Fitzhugh.
  • The interface to the HapMap GBrowse track is courtesy of Simon Twigger.
  • PLINK is the work of Shaun Purcell at the Center for Human Genetic Research of Massachusetts General Hospital

Source Code

Haploview is an open source project hosted by SourceForge. The source can be downloaded at the SourceForge project site.


Haploview can be cited with the following paper:

Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis andvisualization of LD and haplotype maps. Bioinformatics. 2005Jan 15 [PubMed ID: 15297300]

Information about the exact test for HW can be found in the following paper:

Wigginton JE, Cutler DJ, Abecasis GR. A note on exact tests of Hardy-Weinberg equilibrium. Am J Hum Genet. 2005 May;76(5):887-93.

Information about parenTDT can be found in the following paper:

Purcell S, Sham P, Daly MJ. Parental phenotypes in family-based association analysis. Am J Hum Genet. 2005 Feb;76(2):249-59.

Questions, complaints and suggestion should be directed to

System Requirements

It is recommended that Haploview be run on a machine with at least 128M of memory. The Haploview jar file should now automatically allocate extra memory when starting up, so the -Xmx flag is no longer required when running the program from the command line.

Haploview requires Java JRE 1.3 or later, but 1.4 is strongly recommended. It is worthwhile in any case to download the most recent Java release.


If you have an internet connection, Haploview will automatically check for an update upon startup. If a new version is available, it will show a message in the lower right corner of the screen for a few seconds. Details can be found by using the "Check for Updates" button in the File menu.