I was working on a problem involving Heidelbergensis, and it dawned on me that local alignment, and global alignment, are fundamentally different problems. Specifically, if you want to find an optimum global alignment for mtDNA, you can shift the genome incrementally, and compare it to some reference genome, until you maximize the number of matching bases. If you do this locally, the arguably correct way to do this, is to treat every base index, as a potential insertion or deletion. This is intractable, despite the fact that mtDNA is finite. This is obviously not a sensible way to attack the problem. In fact, because you’re definitely going to get non-linear changes in match count as a function of shifting, there’s no way that a generalized optimization algorithm will solve this problem. This implies that as a general matter, global alignments are the correct way to align mtNDA.