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Subler
http://social.wakoopa.com/software/subler
Subler is an Mac OS X app created to mux mp4 files. The main features are: Creation of tx3g subtitles tracks, compatible with all Apple's devices (iPod, AppleTV, iPhone, QuickTime). Mux video, audio, chapters, subtitles and closed captions tracks from mov, mp4 and mkv. Raw formats: H.264 Elementary streams (.h264, .264), AAC (.aac), AC3 (.ac3), Scenarist (.scc) iTunes metadata editing and tagChimp support.