PdfMasher

PdfMasher

Free
It allows you to convert PDF articles to MOBI or EPUB documents
 
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PdfMasher is a tool that allows you to convert PDF articles (newspaper, academic) to MOBI or EPUB documents. You can sort text elements by Y-position (thus grouping them all together), shift select the elements and flag them as ignored. You can also select PDF footnotes and flag them on the MOBI or EPUB document.

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