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| I found a fix. First I completely uninstalled Mathematica, including the folders in the /Library and ~/Library paths (Mathematica and Wolfram folders). Then I reinstalled Mathematica. This fixed some of the problems, specifically I no longer... |
| The structure of your tree tree is more complicated than my code expects. In addition to tips and branch lengths, your file has entries for node names. For example, one bit of the tree file looks like this: ... |