CLAWS has a more fine-tuned tagset, which can assign over 100 PoS codes to English words. Some find them very helpful, and other criticise that it is unnecessary to have so many codes.
TreeTagger has a much simpler tagset of 30-something codes.
Both tools reportedly can achieve over 95% and higher tagging accuracy, which means both can be used in our PoS tagging tasks.
CLAWS is commercial and TreeTagger free.
If your texts were not ASCII codified, they could be converted with tools without any difficulty. There are a lot of tools or scripts out there. So encoding does not matter in distinguishing the two taggers.