If you have algae, your nitrates and phosphates aren't low. Algae need nitrates and phosphates to survive, and without them, you will have an algae-free tank. What is probably happening is that the algae is growing, and using up the nitrates and phosphates from your water, so it shows a low reading on your test kit. That doesn't mean it's not there, it just means it's getting consumed by the algae right away instead of just hanging around in the water.