Only the first sentence is correct. Also: Aren't you my father? CB
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1. Are you not my father? - very formal and perfectly fine. (You are not = Are you not)
2. Aren't you my father? - Colloquial and perfectly fine again. ('Are you' cannot be contracted, therefore, it's 'Aren't you).
3. Are not you my father? - Better to avoid in my opinion.