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Instructions for installing it and the java runtime environment are:

1) Download the file AlignmentV1_3.jar to your computer. It can be put on the desktop or in any folder you think would be convenient.

2) If the program shows up with the icon for an unknown extension type on your system, then you need to install the java runtime environment. If the jre has already been installed on your system, then you can jump to step 3.

a) If the Java Runtime Environment (jre) is not on your system, you must install it. The jre can be downloaded from http://www.java.com/en/download/index.jsp. You can choose to manually install the jre, in which case, you will have to know your computer's operating system, or you can allow the site to download and install the jre automatically.

b) After the jre has installed, reboot your machine and the program will be ready to run. This step is important. The program will not run after installing the jre until the machine has been rebooted.

3) To run the program, double-click on the AlignmentV1_3.jar icon and the program will run.