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I freshly installed LaTeX on my computer using the ProTeXt bundle. I was able to install everything smoothly, but the program TexStudio didn't auto-configure, like the manual said it would. Using Options>>Configure TexStudio>>Commands I was able to set pointers to most commands, except for dvipdf. I have three choices with regards to the executable for dvipdf (listed in the title of this question). Which one should I choose?

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Short answer: dvipdfmx.

Longer answer: dvipdfmx is an extension of dvipdfm, enabling access to more PDF-specific features. As such, it implements a superset of the features of dvipdfm, and is more powerful. dvipdft is a tool to use dvipdfm to make thumbnails (according to texdoc dvipdft). As such, it's not what you want at all!

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    BTW, in current TeXLive, dvipdfm is dvipdfmx running in a compatibility mode. – Khaled Hosny Sep 23 '12 at 22:48
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    There is dvipdf that's part of the Ghostscript distribution, but it's surely inferior to dvipdfmx. – egreg Sep 23 '12 at 23:12

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