Actually, there are several options for how you use the downloadable versions. For example, on an iPhone or iPad, you can use any or all of the versions. You can open the PDF file in iBooks or in some other app that reads PDFs, such as GoodReader. You can use the .mobi version with the Kindle for iPad or Kindle for iPhone app. But, if you want the version that is clearly intended for the iBooks app, then you should use the ePub version. If you are using a Barnes & Noble Nook, then the ePub version is the one to get. The ePub version also is used by the Kobo and Sony readers.
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