FLV encoding

I want to have video on my website by allowing the users to upload their own videos to the site. Right now we are allowing upload of .avi and .mpeg files using the embed tag. The problem with this method is that it is incompatible with most browsers namely mozilla. It seems to work ok with IE but not any others. My question is this, can FMS encode different video file formats like .avi, .mpeg, .mov etc into .flv on the fly during upload or do I have to encode them myself and then re upload them to the server?