Indeed. The compositing tool of choice for this movie and any other effects-heavy movie from the late '90s well into the 2000s was Shake (by Nothing Real, later bought by Apple). The only competition was Nuke, the in-house tool at Digital Domain. It is the last one standing today, since Apple gave up on the high end.

Interesting anecdote I heard: Shake was up for an Academy Award, but Apple pissed off the wrong customer when they discontinued the Windows version (which was used for The Matrix). I won't name the post house, but the owner reportedly sat on the academy's technical committee and tanked Shake's nomination as punishment. Kinda sucked for the team, who of course were blameless.