J/qtl - Installation Guide

Warranty Disclaimer and Copyright Notice

The Jackson Laboratory makes no representation about the suitability or accuracy of this software for any purpose, and makes no warranties, either express or implied, including merchantability and fitness for a particular purpose or that the use of this software will not infringe any third party patents, copyrights, trademarks, or other rights. The software are provided "as is".

This software is provided to enhance knowledge and encourage progress in the scientific community. This is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

The source code for J/qtl can be found at the source code repository on github

Minimum Requirements

  • Operating System: Windows 8, Windows 8.1 or Mac OS X >= 10.4
  • The memory requirement depends on the size of the input data but a minimum of 512MB memory is recommended.
  • R 3.2.*
  • Java 8 or greater


1. Download and install Java

If you already have Java 8 or greater installed you can skip this step otherwise visit http://www.java.com to download and install the latest version of Java.

2. Download and install R

If you already have R 3.2.* installed you can skip this step, otherwise you should go to http://cran.r-project.org to download and install R 3.2.*.

3. Download the J/qtl ZIP file

After ensuring that the correct versions of Java and R are installed you can click here to download J/qtl

4. Expand the J/qtl ZIP file and start the application

Expand the ZIP file that you downloaded in step 3 (you can usually do this by right clicking on the file and selecting an option to expend or decompress) and double click the j-qtl-1.3.5.jar file to start the application