README for the Java Alignment Viewer 
	Contents:
		Introduction
		JAV.tar File Contents
		System and Browser requirments
		Installating and running JAV on Mac,Unix,and DOS

Introduction:
The Java Alignment Viewer (JAV) is an alignment visualization tool with a simple user interface that graphically displays FASTA formatted alignment data. It is designed for maximum flexibility and works on all major platforms with any type of alignment th
at can be modified to an appropriate text file.
 
The JAV.tar file contains:
	Sample Sequence Files
	JAV.jar 
	JAVforMAC
	minus.gif
	plus.gif
	this README


System Requirements:
Java 1.1 JVM with Swing Library (http://java.sun.com/products/jfc/download.html)
or
Java 1.2 JVM or higher

Browser Requirments:
To run the JAV, you must use a browser with Java support:
Netscape 4.06 or later
Internet Explorer 4 or later
Mac users may need to download the MacOS Runtime for Java (MRJ) from http://devworld.apple.com/java/text/download.html.


Installation:

UNIX:
1. Download and extract the JAV.tar file: "tar -xvf JAV.tar"
2. Run the JAV.jar file: "java -jar JAV.jar"

If the program will not run, first chack that the JDK is correctly installed and that the java classpath is set. 

DOS/Windows:

1. Download and extract the JAV.tar file.
2. At the command prompt, run the JAV.jar file: "java -jar JAV.jar"

If the program will not run, first chack that the JDK is correctly installed and that the java classpath is set.

Mac:

1. Extract the JAV folder from the .tar download. This can be done with the most recent version of the freely available program Stuffit Expander.
(http://www.aladdinsys.com/expander/expander_mac_login.html)
2. Find the program "JAVforMac" inside the folder "Mac"
3. Double-click it. 

If you do not have the Java Virtual Machine installed, it is available from: http://devworld.apple.com/java/text/download.html

Mac Runtime for Java (MRJ) 2.2.3 is Apple's implementation of the Java Virtual Machine (JVM), based on Sun Microsystems' Java 1.1.8 specification.