I've been giving this some thought.
Converting to lowercase would clobber (overwrite/obliterate) 11 characters, many of which are quite important. In four instances it means overwriting common characters (lowercase) with rare characters (uppercase). Actually, it depends on how you are doing it. If you are simply adding the uppercase to the lowercase then it would be adding a few common characters that don't exist... but... that doesn't solve the problem in the case of the benched chars EVA-P and EVA-T. They would be lost, subsumed into EVA-p and EVA-t (the same with EVA-k) and the distinction between benched and unbenched might be important (they are not rare chars).
The EVA-u char is very rare. It doesn't have to be included in an analysis of the overall text. That makes one slot available that is not going to skew results. The same for EVA-z. It occurs only three or so times in the whole manuscript. That's two slots. EVA-O (uppercase) isn't needed either.
Would you like me to post an alternate mapping that would enable you to collapse to lowercase without these problems?
Converting to lowercase would clobber (overwrite/obliterate) 11 characters, many of which are quite important. In four instances it means overwriting common characters (lowercase) with rare characters (uppercase). Actually, it depends on how you are doing it. If you are simply adding the uppercase to the lowercase then it would be adding a few common characters that don't exist... but... that doesn't solve the problem in the case of the benched chars EVA-P and EVA-T. They would be lost, subsumed into EVA-p and EVA-t (the same with EVA-k) and the distinction between benched and unbenched might be important (they are not rare chars).
The EVA-u char is very rare. It doesn't have to be included in an analysis of the overall text. That makes one slot available that is not going to skew results. The same for EVA-z. It occurs only three or so times in the whole manuscript. That's two slots. EVA-O (uppercase) isn't needed either.
Would you like me to post an alternate mapping that would enable you to collapse to lowercase without these problems?