After Identification, What's Next?

Now that we can see what changes there have been in DNA sequences, how can we figure out which sequences are more closely related?

Three aligned sequences from the preious slide; A C A G A C dash G A, and A C A T A C A G A, and A C dash T A C dash G A. Three boxes surround the positions where nucleotides are mismatched (not clickable).
The three aligned sequences with three mismatches.