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Using the example staging/stream-trees/ncov-all-clades dataset, zooming into (e.g.) clade 24A and then filtering to just that clade (or vice versa) shows a poorly positioned streamtree:
If you toggle off the filter you can see why the layout is the way it is,
and when we're displaying the tree normally we don't have this problem because we still show an outline of de-selected/filtered nodes:
I don't really know the best solution here. It's not a bug per-se, but it's certainly not ideal!