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Depends on what type of hosting you have. If you have a dedi or VPS, the guide that Barry-xlovecam posted should be helpful to you.
If you're on a shared hosting plan, you are pretty much at the mercy of your host. You can submit a ticket and ask them to install FFMPEG and codecs for you but I have a bad feeling that they will decline your request. FFMPEG, Mencoder, FlvTool, basically all the video stuff can be very resource intensive - particularly CPU and RAM - and could create an unstable hosting environment for other people hosted on the server.
I'm usually pretty surprised when a shared host provides that suite of tools. They need some well-established resource usage policies in place otherwise it usually turns into a clusterfuck.
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