JProfileGrid v1.2.2 Software   Bug correction allows command-line & GUI version to work on very large MSAs. JProfileGrid Documentation
	Requirements JProfileGrid provides both command-line support and a graphical user interface. Software has been been tested on the Macintosh, Windows, and Linux platforms and should work on any system supporting the Java Runtime Environment (JRE) version 5.0 or higher.
	Running JProfileGrid To launch the graphical user interface under MacOS or Windows, double-click on the "JProfileGrid.jar" file icon. Alternatively, for very large alignments (1000's of sequences of average length 300 residues) use the following command in a terminal to give Java more memory: % java -Xmx512M -jar jprofilegrid.jar
	License Software Copyright © 2007 The Regents of the University of California. All Rights Reserved. Permission to use, copy, modify, and distribute this software and its documentation for educational, research, and non-profit purposes, without fee, and without a written agreement is hereby granted, provided that the above copyright notice, this paragraph and the following three paragraphs appear in all copies. Permission to use this software for commercial purposes may be obtained by contacting profilegrid.org. This software program and documentation are copyrighted by The Regents of the University of California. The software program and documentation are supplied "as is", without any accompanying services from The Regents. The Regents does not warrant that the operation of the program will be uninterrupted or error-free. The end-user understands that the program was developed for research purposes and is advised not to rely exclusively on the program for any reason. IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE AND ANY STATUTORY WARRANTY OF NON-INFRINGEMENT. THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF CALIFORNIA HAS NO OBLIGATIONS TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.