How to make the Arduino generate a Clock pulse

Is there a preferred way of getting the Arduino to output a clock pulse for driving an L297 in use for stepper motor control? Or is it just PWM? Normally, my computer's software (EMC2) would be creating this signal but since that doesn't work I want to see if its my computer that doesn't work or the driver for the motor that doesn't work by testing it with a signal generated by an Arduino. And yes, the stepper motor's supply is independent to that of the Arduino :)

Arduino4HS: Is there a preferred way of getting the Arduino to output a clock pulse for driving an L297 in use for stepper motor control?

Probably.

Or is it just PWM?

The ATmega timers are very versatile. They are capable of considerably more than PWM.

Normally, my computer's software (EMC2) would be creating this signal but since that doesn't work I want to see if its my computer that doesn't work or the driver for the motor that doesn't work by testing it with a signal generated by an Arduino.

Seems reasonable.

Have you searched for a stepper library that works with an "L297"? It is possible someone else has already done the heavy lifting.