In this example comparing the sc2ts tree with nextstrain, the root of the clade seems to be quite a bit too recent. I think this is because we're not doing the branch lengths above reversion pushes and mutation coalesces (hereish) in a sensible way. We can verify this by looking at the type of node that the clade root is.
In this example comparing the sc2ts tree with nextstrain, the root of the clade seems to be quite a bit too recent. I think this is because we're not doing the branch lengths above reversion pushes and mutation coalesces (hereish) in a sensible way. We can verify this by looking at the type of node that the clade root is.