BEAST: BAYESIAN ECOLOGICAL ANALYSIS OF STATISTICAL TRENDS
                                                                                                                                          
Beginners to Java

If you're just learning Java, or are interested in learning a little more, there are several very good (and free!) tutorials on the market. Two that I have found to be the best are

Sun's Java Tutorial

Rusty Harold's Cafe au Lait


For advanced programmers who wish to speed things up with the JNI interface (to C or C++), check out Beth Stearns' excellent tutorial.


For Developers

1. Once you have downloaded the zip file of Java files to your hard drive, open the files with any IDE of your choice - I happen to use BlueJ, which is great for beginners: http://www.bluej.org/. BlueJ is great for several reasons - (1) it doesn't contain all of the garbage generate by other IDEs (e.g. Borland), (2) it allows you to visualize the relationships between your Java classes, and (3) it creates runnable Jar files (enabling you to skip step #3 below).

2. Once the files have been compiled, it's pretty easy to create a *.jar file. From the DOS command prompt, use the command "jar cvf beast.jar *.class RngPack/*.class"

3. If you want to distribute the package to people who haven't dowloaded the JRE from Sun, you'll want to make the file executable. To do this, the jar file you created above needs to be Runnable. Shawn Silverman has put together a great how-to page on JavaWorld, complete with instructions and code. Get it here. (if you need help with actually making your jar runnable, let me know).

4. In order to make the runnable jar file executable, you need to have some sort of executable wrapper.  I've experimented with several, and found the free program JSmooth to work well.  If you've followed all of the right steps, the beast.exe file should now run BEAST.