JLIN Download Page

JLIN is available as a downloadable Java Application. JLIN requires Java Runtime Environment 1.5.0 or greater installed on your machine.

The manual for JLIN contains full instructions on how to setup Java and JLIN, input procedures, the results produced and the interface, along with the underlying statistical methods used. The manual is included with the JLIN installer, but is also available as a separate download below.

	JLIN_1.6.0_Install.jar	2.5MB	Java-based installer for all users
	JLIN_1.6.0_Manual.pdf	0.5MB	JLIN User Manual
	JLIN_Example.csv	0.1MB	Example of JLIN's output

Note: Internet Explorer may want to save the above .jar file as a .zip file. In this case, please rename the extension to .jar after it has finished downloading.

Installation Guide

1. Install Java - If you don't already have Java installed, download the latest version of the Java Runtime Environment (JRE). If you're not sure whether or not it has already been installed on your computer, visit www.java.com and click the "Do I have Java?" link. Once finished, you're ready to set up JLIN.
2. Install JLIN - If you're using Windows, double-click on the .jar file you downloaded from above. Alternately, and for non-Windows platforms, simply run a MS-DOS prompt or command prompt and go to the directory where you saved the JLIN_<version>_Install.jar file to (eg cd downloaddir). Now type the following to start the JLIN installer:

         java -jar JLIN_<version>_Install.jar

   The JLIN installer looks and functions the same as any Windows installer (on any platform). Simply follow the on-screen instructions, where you pick the directory to install to, pick whether or not to install the JLIN manual, and then decide where you would like short-cuts to JLIN installed.

3. Run JLIN - On Windows platforms simply click on the short-cut or start-menu item created with the JLIN installation. Alternately, start an MS-DOS or command prompt and go to the directory where JLIN is installed. Now type:

         jlin.bat

   On Linux and non-Windows platforms, use your command shell (terminal) and change to directory where JLIN in installed. Now type:

         ./jlin (or if that doesn't work, try sh jlin)

4. What if nothing happens? - In the event that JLIN doesnt seem to install, or won't run when you try to run it, please check you have the latest version of Java 1.5 installed. Make sure old versions of Java are removed before installing the new version. Please contact the kcarter@cyllene.uwa.edu.au for further assistance.

Referencing JLIN

If you find this tool useful, or use any graphics produced in publications, please refer to:

Carter KW, McCaskie PA, Palmer LJ. JLIN: A Java based Linkage Disequilibrium plotter. BMC Bioinformatics 2006;7(1):60.