Most of the animals are allied now in order to be able to survive against the humans, although many of them are just random civilians in the background because they're not very useful in combat. Before this massive alliance was formed, what determined if they were allies, enemies, or neutral is how they act in real life. Obviously the ant eaters would be mortal enemies of the ants, bears are pretty much mean to everyone, cats and dogs had a huge struggle (the emotional scars of which still run deep between them despite them being in the same alliance). Rabbits get along with almost everyone although were easy prey at first until they turned all ninja-like in their combat abilities and grew in size to about the size of foxes. The wolves were probably bad guys for a bit so might be mistrusted among many other alliance members and are relatively new members of the alliance. Most of the farm animals were slaughtered early on by the humans to avoid complications, although horses did get away.

Some dogs might still be allied with the humans. Few cats are though.

Another thing; the smarter the animal the less effective this whole scenario is, so it's not like chimps turned into Einstein or anything. Primates will not play a large role in this for whatever reason. Maybe they simply couldn't compete with some other animals now that this has taken place and they lost their primary advantage of intelligence.