OK so I was wrong somewhat. 90% of the software they used they created, which some of it was from they used for Ants....the other 10% was off the shelf of which Maya MAY have been used. Anyway the commercial for Maya would like you to believe Maya was used. The character animation was done with a program they created for Ants to do the facial animation called "Shaper", which they applied to the whole body in Shrek. Basically all the muscles are simulated and the mesh morph is done from the inside out (i.e. if a muscle bulges when it is moved then it morphs the mesh appropriately).