No, there are several tools (windows based) which convert videos much nicer. Most of those video websites don't have an unix-only environment, they share all kinds of technologies and use (e.g.) windows servers to handle the convert jobs.
Does anyone know it? FFmpeg and FFmpeg-php are the only thing I can find... is this what everyone uses to convert uploaded videos to SWF?
as far as i know there's a decision- Video to Flash Console. you can use it on webservers and moreover "run conversion using command line parameters automatically by scheduling or by script calling". i think it's just what you were asking about.
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