add discussion of reconstructing ancestors

[jayoung]

add this discussion to README.md

Ching-Ho takes a different approach when polarizing:
use multiple outgroup species (about 5? includes eugracilis), reconstruct the mel-sim ancestor. Use the ancestor instead of sim (or instead of mel) in my R scripts to run the unpolarized code. This is equivalent to getting the mel-branch-only MK result.

he uses MEGA for this: make a tree from the alignment (nucleotide level, not codon level), reconstruct ancestors, and it will spit out the most likely nucleotide at each site. Alternatively, you could also ask it to tell you probabilities, and perhaps replace any very uncertain positions with N.

he's also curious about IQtree to reconstruct ancestors. PAML is another possibility.