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You mean e-reading program on the iPad? I can tell you what I use, but I don't really do much with regard to annotation, so I can't speak to how well it would serve your purpose. It does strike me that if keeping annotation part of the document, then you would be better off taking the earlier advise of using something like Page, but past that, I'll let someone who does a lot of annotation talk about how well various reader programs handle it.
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