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Yes I use both.
It depends what you want to do really.
Calibre is designed more as somewhere to store all your ebooks and it has lots of options including file conversion, rss feeds, emailing books to your kindle, saving and exporting your ebook library ...
Kindle for PC is something I use to read my Kindle books on my PC. Originally I wasn't sure if I'd use it but I find it very handy for the odd read while using the PC and also for looking things up in books like recipes etc
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