Naming Convention for a Quadruped Skeleton in Motion Builder:
Motion Builder 5 comes with a cat skeleton. I exported this skeleton and imported it into Maya 5 as an .fbx file. I used it as a base to create my dog skeleton. The following joint naming structure should be followed to the letter if you want your skeleton to properly "characterize" within Motion Builder.
View a picture of Motion Builder 5's cat skeleton.
The top node is always called "Reference" and is not a joint, but simply a group node.
View a schematic showing the names for the joints and their Parent/Child relationships.
I had to add a tail to my skeleton, remove the jaw on the MB skeleton, and remove all toes but the middle one on each foot for my dog skeleton.