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Many engine options can be modified via the configuration window shown by the chess GUI.
Below a screen shot of the configuration window in Arena 3.5.
The same configuration window in the Shredder Classic 4 GUI:
Note that some GUIs will hide options that are handled elsewhere in its interface. For example, in the second screen shot above the options "Hash", "Ponder", "MultiPV" and "UCI_Chess960" are missing from the configuration window.