GPMAP

GPMAP has been developed based on the open source code of Haploview (ver. 4.1). Therefore GPMAP basically inherits all Haploview functions plus the global partitioning method (Ref).

Java Runtime Environment

Before you'll be able to use Haploview, you'll need two pieces of software: The whole package of Haploview + GPMAP and the Java Runtime Environment (JRE). Get the newest version of the JRE at:

http://www.java.com/

Advanced users can find a variety of older versions of the JRE, plus additional development files at the Java developers website.

How to run the program

Download the following JAR file and click on "Haploview.jar". The program will be simply run if the JAR extention is associated with JRE on your machine.

The program can be run also by typing
java -jar Haploview.jar
on command line.

Download

The following files are available for download:

  • Executable JAR file, Haploview+GPMAP
  • Complete source, GPMAP.zip

    • Documents

    A user guide manual is being prepared and will be presented soon. However, the users familiar to Haploview might easily find how to invoke new features by Haploview + GPMAP package.

    Sample Input

    The complete source includes many samples selected from HapMap ENCODE dataset. Although, you can get them directly from here. Note that these samples should be applied for "Haps Format" tab in the load dialog box starting the software.

    Reference

    Katanforoush A, Sadeghi M, Pezeshk H, Elahi E. Global haplotype partitioning for maximal associated SNP pairs. BMC Bioinformatics, 10(1):269, 2009.

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