Remove .txt, add command line instruction

diff --git a/README.txt b/README
similarity index 53%
rename from README.txt
rename to README
index 07cbd0a..2f4ddec 100755 (executable)
--- a/README.txt
+++ b/README
@@ -1,9 +1,9 @@
-Jalview Release 2.0\r
+Jalview Release 2.01\r
 -------------------\r
 \r
 \r
 \r
-This is the complete source for Jalview 2.0. \r
+This is the complete source for Jalview 2.01. \r
 \r
 The source is available as a tar file and comes complete with the GNU General Public License. \r
 \r
@@ -13,4 +13,16 @@ An Ant build file (build.xml) is provided, you will need to install Apache Ant f
 \r
 You can also use Borland JBuilder to build Jalview. A JBuilder project file (JalviewX.jpx, JalviewApplet.jpx) for both application and applet is provided.\r
 \r
-For more help, read the file doc/building.html
\ No newline at end of file
+For more help, read the file doc/building.html\r
+\r
+\r
+##################\r
+\r
+To run application:\r
+\r
+java -Djava.ext.dirs=JALVIEW_HOME/lib -cp JALVIEW_HOME/jalview.jar jalview.bin.Jalview\r
+\r
+Replace JALVIEW_HOME with the full path to Jalview Installation Directory. If using Windows, use backslash "\" instead of forward slash "/"\r
+\r
+##################\r
+\r