Some people claim to do their vocal tuning in Pro Tools by actually redrawing the waveforms with the Pencil tool. There are maybe 2 people in LA who are so good at this that they get a large portion of the majors' vocal tuning work (or so the legend goes). I myself am skeptical that this can be done, having worked at Digidesign and with Pro Tools extensively. It's fairly simple to adjust the amplitude of a wave (vertically) in Pro Tools, to correct a clip for example, but you would have to be extremely sharp with math, and have a lot of time, to adjust the actual wavelengths (horizontally) and come out with a result that is correct. I suspect that what they really do is tune on a note-by-note, word-by-word, or phrase-by-phrase basis with a manual pitch correction plugin such as the one included with Pro Tools.