Adding References

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I'm creating an ebook version of a book on nutritional science, which contains over 200 references. My first instinct is to use EndNote, BibDesk, or a similar program to insert the references in-text with hyperlinks to a reference list at the end of the book. However, I was unsure if this was the best method (or even possible) with epub. I'm sending the completed ebook in HTML format to an independent publisher friend who is going to put it on amazon for me, so I'm not as worried about getting it totally perfect, but I want to be sure that the references will look correct in-text if I use a reference management program, and will link to the full reference.

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