| abouheif | Compute the Abouheif distance matrix |
| chisq_test | Perform Chi-Square Test on Sets of Transmission Trees |
| euclidean | Calculate the Euclidean distance between two distance matrices. |
| kendall | Compute the Kendall distance matrix |
| make_tree | Generate a Transmission Tree |
| patristic | Compute the Patristic distance matrix |
| permanova_test | Perform PERMANOVA on Sets of Transmission Trees |
| shuffle_graph_ids | Shuffle Node IDs in a Graph |
| tree_test | Test Differences Between Sets of Transmission Trees |
| validate_tree | Validate a Transmission Tree |