swapWithUncleAlignToParent() now makes use of upper tree info. On the
5-sequence glob_25 set this obviously doesn't make a massive difference
in many cases, but there are some cases where it improves the proposals.

Next is to implement the same type of scheme for fastSwapWithUncle,
using two hmm2Align calls rather than two hmm3Align calls (and a
possible hmm2Align). The combination of preserving anchors and fewer
realignments, plus extra tree information, will hopefully result in more
favourable proposals.