For best results use a Sun java run time environment (not the gcj gnu java, sorry!).
-If you want to the java runtime bundled with Jalview, then launch jalview like this:
+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
-[or
+
+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
-in macOS]
+
+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'
##################