@Valorum's answer is correct in that it states that, that Alice is the real one. However, it has been revealed in Resident Evil: The Final Chapter that Alice herself is a clone of Alicia Marcus. Alicia is the daughter of Professor James Marcus, the creator of the Umbrella Corporation.
Dr Isaacs: I'm Dr. Alexander Roland Isaacs. The original.
Alice: The one I met out there, he thought exactly the same thing.
Dr Isaacs: Of course he did. That's how they're designed. They always try harder and fight longer even to death as long as they think they're the real thing. After all, who wants to know they're just a poor imitation, or a worthless copy? Which brings us to you.
Dr Isaacs: Oh come now. You thought you were the original. How delicious. No, I'm afraid she holds that dubious honor. Alicia Marcus, daughter of my old partner, James. Co-owner of the Umbrella Corporation and a painful thorn in my side. What I now intend to remove.
Alicia: Time, is running out, Alice. You must kill him soon.
Dr Isaacs: It's good to see you too, Alicia. Marcus created the T-Virus to save her but the effects didn't last. I've been waiting years for her to die.
Alice: I'm not... I'm not a clone.
Dr Isaacs: Really? You must've wondered why you remember nothing of your childhood. Your father. Your mother.
Alice: Memory loss.
Dr Isaacs: No. You have no memory because you had no life. Nothing before the mansion, when we created you, 10 years ago.
Alice: I know who I am.
Dr Isaacs: I don't think so. You're nothing more than a puppet whose strings were cut. And then you wandered around for a little while thinking you were a real girl. But you're not. You're just a clever imitation. A facsimile. A rather troublesome one at that.
Alice: You're lying to me.
The Red Queen: I'm afraid he's not. You were created in her image, as was I.
Resident Evil: The Final Chapter