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I have a program that captures and stores H.264 encoded video as well as audio into a proprietary format file. I need to be able to export that video and audio to an mp4 file. I prefer C# but will use C++ if necessary. Any suggestions?

Mishka
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To produce MPEG-4 Part 14 .MP4 file you need a multiplexer. There is a choice of multiplexers out there:

API and complexity might vary because some of multiplexers are expected to be a part of pipeline, they are not completely standalone classes. You might want to check respective samples (and license agreements, perhaps, too) to see what is best for you.

Roman R.
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Take a look at libmp4v2. Fairly straightforward to use..

http://code.google.com/p/mp4v2/