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The Kindle application uses the built-in Safari browser on the iPad to purchase content through the amazon.com website.
Ibis Reader is a unique application because it is written in HTML5 and is a cross-platform EPUB reader that will work on iPad, iPhone, Android, and many other web-enabled devices. It has the ability to connect to remote content libraries that use the OPDS format which includes Feedbooks, the Internet Archive Book Catalog, Smashwords, the Pragmatic Bookshelf, as well as personal OPDS catalogs that you may wish to host on your own Cloud storage, such as on Dropbox.
The Ibis reader website allows you to directly upload EPUB content or connect to remote OPDS book repositories.