How do i do that?
i dont think you can, though some said that quicktime allows you to do this, as im on linux quicktime isnt an option to me, use tga, png, or better multilayer.
You can get transparent movies with Quicktime (probably need pro version). As other have said, save the animation as png with alpha channel; import the file sequence into quicktime; go to the show movie properties window; click on video track and visual settings; in the transparency box select straight alpha and save as a quicktime movie. I don’t think you can compress the file and maintain alpha transparency though.