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| comp.freq | Compare Model Probabilities to Frequencies |
| convert | Converts Matrix to Newick Format |
| is.tree | Compare with Tree Format |
| kidney | Cytogenetic data from kidney carcinoma |
| MLparameters | Compute Maximum Likelihood Parameters |
| MLtopology | Compute Maximum Likelihood Tree Topology |
| mrca | Most Recent Common Ancestor |
| subtree | Subtree |