The Alien base is part of Army of ages which it's not part of the same base like the others, it changes every time a alien evolves and new aliens come into the battle field. The base has 50,000 hp so it takes awhile to attack.
Unlike the usual human base, the alien nest is where the invading aliens are spawned or birthed. One tip that can lead to winning the game easier is to mass produce ranged units while using melee units as cover. The ranged units will ignore the defending aliens and will focus on the nest if they are within the range of the nest. Be very careful though, as the alien nest has the ability to evolve and create kamikaze aliens which will not hesitate to wipe out your front line units, or your ranged units.