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need to convert videos to flv on my Red5 server.Any help in this regard will be very helpful.

+1  A: 

I use ffmpeg on my Ubuntu box with great results.

svn checkout svn://svn.ffmpeg.org/ffmpeg/trunk ffmpeg

A: 

There was a project created by Dan Fernandez on Coding4Fun which uses FFMPEG to convert flv to mpeg, the reverse is also true.

Here is the project he created called InnerTube

Here is the link to a site detailing the command line arguments with FFMPEG.

Chris