If the squat is troublesome for you, the best alternative exercises to consider are exercises that mimic either the joint action or muscle groups involved in the squat.
Scientists discovered that towing a weighted sled with about 13% of your body weight can improve a 30m sprint significantly. Time to bust out some weights and start dragging!
A recent study compared the effects of combined weighted sled training and sprint training against traditional sprint training on 10 and 30 meter speed in professional rugby players.
Chris Duffin, champion powerlifter, demonstrates one of his favorite conditioning/assistance movements - the sled pull-through. This is an intense exercise for the posterior chain.