Any professional-level program will let you shift keys and rhythms, and allow for unusual times like 5/4 (not so unusual since Stravinsky). My cheap little DOS music-writing program, SongWright, will let you do that.

But there are more complex things it's harder to do this way on a computer (have you ever seen a score of George Crumb's? Yikes!), and most people just won't bother.