It is not trivial to correct for "multiple hits", i.e. convert from observed base changes to branch lengths, because mutations are super concentrated in a relatively small fraction of the positions. This has the result that the simulation doesn't accurately reproduce really high (30-35%) mutation levels (it shifts them to somewhat lower levels).
It is not trivial to correct for "multiple hits", i.e. convert from observed base changes to branch lengths, because mutations are super concentrated in a relatively small fraction of the positions. This has the result that the simulation doesn't accurately reproduce really high (30-35%) mutation levels (it shifts them to somewhat lower levels).