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There are several programs that emulate keyboard and mouse input with a gamepad such as JoyToKey, Xpadder, Pinnacle Game Profiler and Enjoy2. If your controller is not recognized, a turnaround to make it work for this emulator is to use a tool that will bind your keyboard's keys to your controller. I didn't have any issues with generic controllers that look like PS2 controllers, while my wireless xbox360 controllers would not be recognized.
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Some USB controllers are supported by this emulator, others are not. You can change the button to key mapping for both players in the emulator by going to "Options/Input Configuration" or switch from the keyboard to controller(s).
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