-\r
-##################\r
-\r
-\r
-\r
-\r
-If you use a proxy server add \r
-\r
--Dhttp.proxyServer=YOUR.SERVER -Dhttp.proxyPort=YOURPORT\r
-\r
-If the proxy server requires authentication, add\r
-\r
+Use -help to see the available command line arguments.
+
+For best results use a Sun java run time environment (not the gcj gnu java, sorry!).
+
+If you want to use the java runtime bundled with Jalview, then launch jalview like this:
+
+in Windows:
+JAVA_HOME=JALVIEW_HOME/jre JALVIEW_HOME/jre/bin/java -classpath "JALVIEW_HOME/lib/*;JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
+
+in Linux:
+JAVA_HOME=JALVIEW_HOME/jre JALVIEW_HOME/jre/bin/java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
+
+in macOS:
+JAVA_HOME=JALVIEW_HOME/jre/Contents/Home JALVIEW_HOME/jre/Contents/Home/bin/java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
+
+Note: ensure the -classpath argument is quoted and only use a terminating wildcard (e.g. 'DIR/*') to refer to all jar files in a directory, don't use e.g. 'DIR/*.jar'
+
+##################
+
+
+If you use a proxy server add
+
+-Dhttp.proxyServer=YOUR.SERVER -Dhttp.proxyPort=YOURPORT
+
+If the proxy server requires authentication, add
+