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VLC player and totem video player can't play MSS2 video encoded video files but i could play them under Ubuntu by compiling FFMPEG library. now ffplay can play these files. My question is if there is any way to add these codecs to system so that vlc player or totem video player can also play these files. i tried "sudo make install" in my ffmpeg folder but it seems it has no effect on system codecs. thank you.

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VLC is using the fork Libav instead of your FFmpeg. You did not mention your Ubuntu version, but Libav as of Ubuntu 13.10 does not support MSS2 (MS Windows Media Video V9 Screen) decoding. You compile VLC to use recent FFmpeg as shown in:

Howto: Compile the development version of vlc under the latest Ubuntu release

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