API for Hoffmann-Lab/PhyloEpiGenomics
What the Package Does (One Line, Title Case)
| Global functions | |
|---|---|
| all_fitch_margoliash | Source code |
| all_parsimony | Man page Source code |
| all_rooted_tree_topologies | Source code |
| all_unrooted_tree_topologies | Source code |
| best_fitch_margoliash | Source code |
| branch_fractions_to_lengths | Source code |
| discretize | Source code |
| estimate_kappa | Source code |
| exchange_states | Source code |
| find_each_optimal_tree | Source code |
| find_optimal_tree | Source code |
| fitch_margoliash | Source code |
| get_distance_log_likelihood | Source code |
| get_node_likelihoods_formula | Source code |
| get_tree_log_likelihood | Source code |
| get_tree_log_likelihood_formulas | Source code |
| initialize_clock_tree_branch_fractions | Source code |
| intersect_intervals | Source code |
| make_evolutionary_model | Source code |
| make_states_alignment_compact | Source code |
| make_tree_from_branch_fractions | Source code |
| maximize_clock_tree_log_likelihood | Man page Source code |
| maximize_distance_log_likelihoods | Source code |
| maximize_tree_log_likelihood | Source code |
| maximize_tree_log_likelihood_extended | Source code |
| maximum_parsimony | Man page Source code |
| simulate_evolution | Man page Source code |
| simulate_evolution_node | Source code |
| small_parsimony | Man page Source code |
| small_parsimony_bottom_up | Source code |
| small_parsimony_costs | Source code |
| small_parsimony_top_down | Source code |
| tree_to_distance_matrix | Source code |
| tree_to_distances | Source code |
