Actually, both are written ALL together. separate and altogther... ;-) From dictionary.com altogether –adverb 1. wholly; entirely; completely; quite: altogether fitting. 2. with all or everything included: The debt amounted altogether to twenty dollars. 3. with everything considered; on the whole: Altogether, I'm glad it's over. —Idiom 4. in the altogether, Informal . nude: When the phone rang she had just stepped out of the bathtub and was in the altogether.

You mean the older spelling of together? "to-gether" :) We got rid of the hyphen because it looked awful. Funnily, if you look at the history of both words you find they have 'unnecessary' chunks. The "se-" in separate already means "apart" ("-parate" has to do with cutting), and the "-gether" in the adverb together already means... umm, "together" (related to the verb "gather").