java -Djava.ext.dirs=JALVIEW_HOME/lib -cp JALVIEW_HOME/jalview.jar jalview.bin.Jalview
-Replace JALVIEW_HOME with the full path to Jalview Installation Directory.
+Replace JALVIEW_HOME with the full path to Jalview Installation Directory. If building from source:
+
+java -Djava.ext.dirs=JALVIEW_BUILD/dist -cp JALVIEW_BUILD/dist/jalview.jar jalview.bin.Jalview
+
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