Is there any difference between the following sentences
Are you not my father?
Are not you my father?
Which sentence is more natural?
Only the first sentence is correct. Also: Aren't you my father?

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Oops! I thought both were correct but had different meanings.
"Sir, are not you my father?" I have read this line in Shakespeare's Tempest, Act I-scene II spoken by Miran. Do you think he could use incorrect English or I'm facing a typo mistake?
Shakespeare lived 400 years ago. English has changed a lot since then.

Yes, you are write English has changed a lot since then. But we can't say anything wrong written by the legends like Shakespeare. I heard people often call them Old English or Shakespearean English.
Anyway thanks for your help.
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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.