Zaius asked why it was dumb to just add up the unique sequence from each species to get the total divergence. Here's why. Consider two sequences, each 20 bp long:
----------ACGGTTCCGATTTTTTTTTT
CCCCCCCCCCACGGTTCCGA----------
The dashes are sequence that doesn't exist in that copy. 10 out of the 20 bp in each sequence are identical and ten are different. 50% of the sequence in each is unique to that copy (e.g. represents an insertion in its lineage). If we add up the fraction of unique sequence in both, we conclude that they have 0% of their bases in common, even though they are 50% identical.
That is dumb.
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