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Minor suggestion (I know this isn't a main issue, and it's still early in coding) but the convention in phylogenetics is to draw an unresolved group as a triangle rather than a box (with a short subtending edge, as you already do). See, for example, <http://vsmith.info/files/papers/fossil/download/Fig2.jpg >. This will make your prototype look less "weird" to a biologist.
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