Replaced battery on a 99 f-250 it will not start alarm goes on

Does the starter motor crank the engine OK?
If so, have a helper crank it while you check for spark at the plugs, gasoline engine. Also, check proper fuel pressure and fuel injector pulse.
Sometimes when battery voltage is lost, it can effect your security system. If that is the problem, you may need a scanner that can communicate with security system in order to fix. Just my opinion.