DOS(Box): Setmain.exe -> Controller Setup -> Setup Keyboard
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Eduke32: Start the game -> Options -> Keyboard Setup
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XDuke: Start the game -> Options -> Setup Keyboard
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I recommend you use
EDuke32 for single player gaming and
XDuke for multiplayer games.
And if you want to play multiplayer games, install
YANG and/or
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If you use EDuke32 you can also use the high resolution packs: