end gap separation penalty setting specification End Gap Separation: Treats end gaps just like internal gaps for the purposes of avoiding gaps that are too close (set by GAP SEPARATION DISTANCE above). If you turn this off, end gaps will be ignored for this purpose. This is useful when you wish to align fragments where the end gaps are not biologically meaningful. A software execution setting specification that states whether or not to apply the gap extension penalty when scoring terminal gaps using a Boolean value. configuration parameter which is a Boolean value, that states whether or not to apply the gap extension penalty when scoring terminal gaps. end gap separation penalty ClustalW Web service Documentation and WS annotations Group, UGA WS Annotations Group, UGA software execution setting specification