| ABC_MCMC |
Source code
|
| ACF_continuous_trait_CPP |
Source code
|
| ACF_spherical_CPP |
Source code
|
| ASR_binomial_CPP |
Source code
|
| ASR_via_independent_contrasts_CPP |
Source code
|
| ASR_via_squared_change_parsimony_CPP |
Source code
|
| ASR_with_fixed_rates_Markov_model_CPP |
Source code
|
| CDF_from_samples |
Source code
|
| CR_HBD_model_loglikelihood_CPP |
Source code
|
| HBD_PDR_loglikelihood_CPP |
Source code
|
| HBD_PSR_loglikelihood_CPP |
Source code
|
| HBD_model_loglikelihood_CPP |
Source code
|
| Mk_loglikelihood_CPP |
Source code
|
| SBM_LLs_of_sampled_transitions_CPP |
Source code
|
| SBM_LLs_of_transitions_CPP |
Source code
|
| SBM_get_SBM_PD_functor_CPP |
Source code
|
| SBM_get_average_transition_angle_CPP |
Source code
|
| TR_Mk_loglikelihood_ICs_CPP |
Source code
|
| TSBM_LL_of_sampled_transitions_CPP |
Source code
|
| TSBM_LL_of_transitions_CPP |
Source code
|
| WMPR_ASR_CPP |
Source code
|
| all_pairwise_geodesic_angles |
Source code
|
| apply_BM_parsimony_to_missing_clades_CPP |
Source code
|
| apply_attributes_to_descendants_CPP |
Source code
|
| apply_fixed_rate_Markov_model_to_missing_clades_CPP |
Source code
|
| asr_empirical_probabilities |
Man page
Source code
|
| asr_independent_contrasts |
Man page
Source code
|
| asr_max_parsimony |
Man page
Source code
|
| asr_mk_model |
Man page
Source code
|
| asr_squared_change_parsimony |
Man page
Source code
|
| asr_subtree_averaging |
Man page
Source code
|
| assign_clades_to_taxa |
Source code
|
| assign_clades_to_taxa_CPP |
Source code
|
| assign_points_to_tiles_on_sphere |
Source code
|
| back |
Source code
|
| bootstrap_Kolmogorov_Smirnov_test |
Source code
|
| bootstraps_to_confidence_intervals |
Source code
|
| calculate_equal_tailed_CIs_of_curves |
Source code
|
| castor |
Man page
|
| castor-package |
Man page
|
| check_biom_json_validity |
Source code
|
| clade_densities |
Man page
Source code
|
| collapse_monofurcations |
Man page
Source code
|
| collapse_tree_at_resolution |
Man page
Source code
|
| collapse_tree_at_resolution_CPP |
Source code
|
| completement |
Source code
|
| compress_musse_params |
Source code
|
| congruent_divergence_times |
Man page
Source code
|
| congruent_hbds_model |
Man page
Source code
|
| congruify_trees |
Source code
|
| congruify_trees_CPP |
Source code
|
| consensus_taxonomies |
Man page
Source code
|
| consensus_taxonomies_CPP |
Source code
|
| consentrait_depth |
Man page
Source code
|
| correlate_phylo_geodistances |
Man page
Source code
|
| count_clades_at_regular_times_CPP |
Source code
|
| count_clades_at_times_CPP |
Source code
|
| count_lineages_through_time |
Man page
Source code
|
| count_lineages_through_time_BD |
Source code
|
| count_tips_per_node |
Man page
Source code
|
| count_transitions_between_clades |
Man page
Source code
|
| count_transitions_between_clades_CPP |
Source code
|
| date_tree_red |
Man page
Source code
|
| date_tree_via_RED_CPP |
Source code
|
| dbeta4 |
Source code
|
| dense_binary_matrix_row2column_major_CPP |
Source code
|
| derivatives_of_grid_curve_CPP |
Source code
|
| discrete_trait_depth |
Man page
Source code
|
| draw_SBM_geodesic_angle_CPP |
Source code
|
| eliminate_bifurcating_root |
Source code
|
| eliminate_bifurcating_root_CPP |
Source code
|
| ensure_uncompressed |
Source code
|
| evaluate_spline |
Man page
Source code
|
| evaluate_spline_CPP |
Source code
|
| evaluate_univariate_expression |
Source code
|
| evaluate_univariate_expression_CPP |
Source code
|
| expanded_tree_from_jplace |
Man page
Source code
|
| expected_SBM_distance |
Source code
|
| expected_distances_sbm |
Man page
Source code
|
| exponentiate_matrix |
Man page
Source code
|
| exponentiate_matrix_for_multiple_scalings_CPP |
Source code
|
| extend_tree_to_height |
Man page
Source code
|
| extend_tree_to_height_CPP |
Source code
|
| extract_HBDS_events_from_tree |
Source code
|
| extract_deep_frame |
Man page
Source code
|
| extract_deep_frame_CPP |
Source code
|
| extract_fasttree_constraints |
Man page
Source code
|
| extract_fasttree_constraints_CPP |
Source code
|
| extract_independent_rates_from_transition_matrix |
Source code
|
| extract_independent_rates_from_vector |
Source code
|
| extract_tip_neighborhood |
Man page
Source code
|
| extract_tip_neighborhood_CPP |
Source code
|
| extract_tip_radius |
Man page
Source code
|
| fill_gaps_in_integer_state_list |
Source code
|
| find_edge_splitting_tree |
Source code
|
| find_edge_splitting_tree_CPP |
Source code
|
| find_farthest_tip_pair |
Man page
Source code
|
| find_farthest_tips |
Man page
Source code
|
| find_nearest_tips |
Man page
Source code
|
| find_non_zeros_float_CPP |
Source code
|
| find_non_zeros_int_CPP |
Source code
|
| find_root |
Man page
Source code
|
| find_root_for_monophyletic_clade_CPP |
Source code
|
| find_root_of_monophyletic_tips |
Man page
Source code
|
| first_Wasserstein_distance |
Source code
|
| first_Wasserstein_distance_CPP |
Source code
|
| first_derivative |
Source code
|
| fit_OU1_model |
Source code
|
| fit_SBM_diffusivity_from_transitions_CPP |
Source code
|
| fit_SBM_from_sampled_transitions_CPP |
Source code
|
| fit_and_compare_bm_models |
Man page
Source code
|
| fit_and_compare_sbm_const |
Man page
Source code
|
| fit_bm_model |
Man page
Source code
|
| fit_exp_LeastLogSquares_moving_window_CPP |
Source code
|
| fit_exp_Poisson_moving_window_CPP |
Source code
|
| fit_hbd_model_on_best_grid_size |
Source code
|
| fit_hbd_model_on_grid |
Man page
Source code
|
| fit_hbd_model_parametric |
Man page
Source code
|
| fit_hbd_pdr_on_best_grid_size |
Man page
Source code
|
| fit_hbd_pdr_on_grid |
Man page
Source code
|
| fit_hbd_pdr_parametric |
Man page
Source code
|
| fit_hbd_psr_on_best_grid_size |
Man page
Source code
|
| fit_hbd_psr_on_grid |
Man page
Source code
|
| fit_hbd_psr_parametric |
Man page
Source code
|
| fit_hbds_model_on_best_grid_size |
Source code
|
| fit_hbds_model_on_grid |
Man page
Source code
|
| fit_hbds_model_parametric |
Man page
Source code
|
| fit_local_exponential_rate |
Source code
|
| fit_mk |
Man page
Source code
|
| fit_musse |
Man page
Source code
|
| fit_sbm_const |
Man page
Source code
|
| fit_sbm_const_biased_sampling |
Source code
|
| fit_sbm_geobiased_const |
Man page
Source code
|
| fit_sbm_linear |
Man page
Source code
|
| fit_sbm_on_best_grid_size |
Source code
|
| fit_sbm_on_grid |
Man page
Source code
|
| fit_sbm_parametric |
Man page
Source code
|
| fit_sbm_trend |
Source code
|
| fit_symmetric_mk |
Source code
|
| fit_tree_model |
Man page
Source code
|
| flatten_list_first_level |
Source code
|
| flatten_musse_params |
Source code
|
| forest_distance |
Source code
|
| gamma_statistic |
Man page
Source code
|
| generate_OU_time_series |
Source code
|
| generate_bounded_BM_time_series |
Source code
|
| generate_gene_tree_in_species_tree_MSC_CPP |
Source code
|
| generate_gene_tree_in_species_tree_MSC_HGT_DL_CPP |
Source code
|
| generate_gene_tree_msc |
Man page
Source code
|
| generate_gene_tree_msc_hgt_dl |
Man page
Source code
|
| generate_random_tree |
Man page
Source code
|
| generate_random_tree_BM_rates_CPP |
Source code
|
| generate_random_tree_CPP |
Source code
|
| generate_random_tree_HBDS_CPP |
Source code
|
| generate_random_tree_Mk_rates_CPP |
Source code
|
| generate_random_tree_OU_rates_CPP |
Source code
|
| generate_random_tree_tdSSE_CPP |
Source code
|
| generate_tree_from_PSR_CPP |
Source code
|
| generate_tree_hbd_reverse |
Man page
Source code
|
| generate_tree_hbds |
Man page
Source code
|
| generate_tree_with_evolving_rates |
Man page
Source code
|
| geodesic_angle |
Source code
|
| geodesic_angles |
Source code
|
| geodesic_angles_CPP |
Source code
|
| geographic_acf |
Man page
Source code
|
| get_Colless_Imbalance_CPP |
Source code
|
| get_HBDS_model_loglikelihood_CPP |
Source code
|
| get_LTT_BD_CPP |
Source code
|
| get_MuSSE_loglikelihood_CPP |
Source code
|
| get_MuSSE_loglikelihood_classic_CPP |
Source code
|
| get_Ornstein_Uhlenbeck_time_series_CPP |
Source code
|
| get_PSR_from_PDR_HBD |
Source code
|
| get_PSR_from_PDR_HBD_CPP |
Source code
|
| get_PSR_of_CR_HBD_model_CPP |
Source code
|
| get_PSR_of_HBD_model |
Source code
|
| get_PSR_of_HBD_model_CPP |
Source code
|
| get_Poisson_event_times_CPP |
Source code
|
| get_Robinson_Foulds_distance_CPP |
Source code
|
| get_SBM_ACF |
Source code
|
| get_SBM_independent_contrasts |
Source code
|
| get_adjacent_edges_per_edge |
Source code
|
| get_adjacent_edges_per_edge_CPP |
Source code
|
| get_all_branching_ages |
Source code
|
| get_all_distances_to_root |
Man page
Source code
|
| get_all_distances_to_tip |
Man page
Source code
|
| get_all_distances_to_tip_CPP |
Source code
|
| get_all_node_depths |
Man page
Source code
|
| get_all_pairwise_distances |
Man page
Source code
|
| get_all_pairwise_geodesic_angles_CPP |
Source code
|
| get_ancestral_nodes |
Man page
Source code
|
| get_ancestral_nodes_CPP |
Source code
|
| get_antiderivative_CPP |
Source code
|
| get_antiderivative_of_splines_function |
Source code
|
| get_bounded_BM_time_series_CPP |
Source code
|
| get_branching_ages_from_LTT |
Source code
|
| get_branching_ages_from_LTT_CPP |
Source code
|
| get_child_count_per_node |
Source code
|
| get_child_count_per_node_CPP |
Source code
|
| get_clade_list |
Man page
Source code
|
| get_closest_tip_per_clade_CPP |
Source code
|
| get_complement |
Source code
|
| get_conditional_transition_probabilities |
Source code
|
| get_congruent_HBDS_CPP |
Source code
|
| get_connected_subgraphs |
Source code
|
| get_derivative_CPP |
Source code
|
| get_derivative_of_splines_function |
Source code
|
| get_discrete_trait_depth_CPP |
Source code
|
| get_distance_matrix_between_clades_CPP |
Source code
|
| get_distances_between_clades_CPP |
Source code
|
| get_distances_from_root_CPP |
Source code
|
| get_diversities_from_birth_and_death_events_CPP |
Source code
|
| get_dummy_graphics_params |
Source code
|
| get_empirical_state_frequencies_per_node_CPP |
Source code
|
| get_expected_SBM_sinsquare |
Source code
|
| get_farthest_tip_pair_CPP |
Source code
|
| get_farthest_tip_per_clade_CPP |
Source code
|
| get_farthest_tips_per_edge_CPP |
Source code
|
| get_file_extension |
Source code
|
| get_flat_musse_param_names |
Source code
|
| get_gamma_statistic_CPP |
Source code
|
| get_incoming_edges_per_clade |
Source code
|
| get_incoming_edges_per_clade_CPP |
Source code
|
| get_independent_contrasts |
Man page
Source code
|
| get_independent_sister_tips |
Man page
Source code
|
| get_independent_sister_tips_CPP |
Source code
|
| get_inhomogeneous_grid_1D |
Source code
|
| get_inhomogeneous_grid_1D_CPP |
Source code
|
| get_inhomogeneous_grid_1D_from_samples |
Source code
|
| get_intersection |
Source code
|
| get_mean_depth_per_node_CPP |
Source code
|
| get_mean_state_per_node_CPP |
Source code
|
| get_member_lists_from_group_assignments |
Source code
|
| get_member_lists_from_group_assignments_CPP |
Source code
|
| get_min_max_tip_distance_from_root_CPP |
Source code
|
| get_most_recent_common_ancestor_CPP |
Source code
|
| get_most_recent_common_ancestors_CPP |
Source code
|
| get_mrca_defining_tips_CPP |
Source code
|
| get_mrca_of_set |
Man page
Source code
|
| get_name_series |
Source code
|
| get_nice_scale_bar |
Source code
|
| get_outgoing_edges_per_clade |
Source code
|
| get_outgoing_edges_per_clade_CPP |
Source code
|
| get_pairwise_ancestries_CPP |
Source code
|
| get_pairwise_distances |
Man page
Source code
|
| get_pairwise_mrcas |
Man page
Source code
|
| get_paths_root_to_tips |
Source code
|
| get_paths_root_to_tips_CPP |
Source code
|
| get_phylogenetic_independent_contrasts_CPP |
Source code
|
| get_phylogram_geometry |
Source code
|
| get_phylogram_geometry_CPP |
Source code
|
| get_radial_tree_geometry_CPP |
Source code
|
| get_random_diffusivity_matrix |
Man page
Source code
|
| get_random_mk_transition_matrix |
Man page
Source code
|
| get_random_params |
Source code
|
| get_rate_index_vector |
Source code
|
| get_reds |
Man page
Source code
|
| get_relative_evolutionary_divergences_CPP |
Source code
|
| get_root_clade_CPP |
Source code
|
| get_smallest_items |
Source code
|
| get_speciation_extinction_events_CPP |
Source code
|
| get_spline_CPP |
Source code
|
| get_stationary_distribution |
Man page
Source code
|
| get_subtree_at_node |
Man page
Source code
|
| get_subtree_at_node_CPP |
Source code
|
| get_subtree_with_clades |
Source code
|
| get_subtree_with_specific_clades_CPP |
Source code
|
| get_subtree_with_specific_tips_CPP |
Source code
|
| get_subtree_with_tips |
Man page
Source code
|
| get_subtrees_at_nodes |
Man page
Source code
|
| get_subtrees_at_nodes_CPP |
Source code
|
| get_sum_of_edge_lengths_per_clade_CPP |
Source code
|
| get_tips_for_mrcas |
Man page
Source code
|
| get_total_tip_count_per_node_CPP |
Source code
|
| get_trait_acf |
Man page
Source code
|
| get_trait_depth_consenTRAIT_CPP |
Source code
|
| get_trait_richness_collectors_curve_CPP |
Source code
|
| get_trait_stats_at_times_CPP |
Source code
|
| get_trait_stats_over_time |
Man page
Source code
|
| get_transition_index_matrix |
Man page
Source code
|
| get_transition_matrix_from_rate_vector |
Source code
|
| get_tree_from_branching_ages_CPP |
Source code
|
| get_tree_from_sampling_branching_ages_CPP |
Source code
|
| get_tree_span |
Man page
Source code
|
| get_tree_traversal_root_to_tips |
Man page
Source code
|
| get_tree_traversal_root_to_tips_CPP |
Source code
|
| get_tree_with_collapsed_monofurcations_CPP |
Source code
|
| guesstimate_Mk_rate_via_independent_contrasts |
Source code
|
| guesstimate_Mk_transition_rates_via_max_parsimony_ASR |
Source code
|
| hsp_binomial |
Man page
Source code
|
| hsp_empirical_probabilities |
Man page
Source code
|
| hsp_independent_contrasts |
Man page
Source code
|
| hsp_max_parsimony |
Man page
Source code
|
| hsp_mk_model |
Man page
Source code
|
| hsp_nearest_neighbor |
Man page
Source code
|
| hsp_squared_change_parsimony |
Man page
Source code
|
| hsp_subtree_averaging |
Man page
Source code
|
| initiate_plot_file |
Source code
|
| is_bifurcating |
Man page
Source code
|
| is_monophyletic |
Man page
Source code
|
| is_monophyletic_tip_set_CPP |
Source code
|
| join_rooted_trees |
Man page
Source code
|
| join_rooted_trees_CPP |
Source code
|
| keep_unique_tip_labels |
Source code
|
| list_to_biom_string |
Source code
|
| load_jplace |
Source code
|
| loglikelihood_hbd |
Man page
Source code
|
| make_biom_table |
Source code
|
| make_matrix_sparse |
Source code
|
| map_tip_or_node_names_to_indices |
Source code
|
| map_to_state_space |
Man page
Source code
|
| match_tree_nodes |
Source code
|
| match_tree_nodes_CPP |
Source code
|
| matrix_from_biom_table |
Source code
|
| mean_abs_change_scalar_ou |
Man page
Source code
|
| merge_nodes_to_multifurcations |
Man page
Source code
|
| merge_nodes_to_multifurcations_CPP |
Source code
|
| merge_short_edges |
Man page
Source code
|
| merge_short_edges_CPP |
Source code
|
| metadata_from_biom_table |
Source code
|
| model_adequacy_hbd |
Man page
Source code
|
| model_adequacy_hbds |
Man page
Source code
|
| monotonize_series_by_pruning |
Source code
|
| monotonize_series_by_pruning_CPP |
Source code
|
| monotonize_series_via_interpolation_CPP |
Source code
|
| monotonize_time_series_via_interpolation |
Source code
|
| move_points_on_sphere_CPP |
Source code
|
| multifurcations_to_bifurcations |
Man page
Source code
|
| multifurcations_to_bifurcations_CPP |
Source code
|
| open_file |
Source code
|
| parent_nodes |
Source code
|
| pick_random_tips |
Man page
Source code
|
| pick_random_tips_CPP |
Source code
|
| place_paired_end_reads |
Source code
|
| place_paired_end_reads_CPP |
Source code
|
| place_sorted_values_into_bins_CPP |
Source code
|
| place_tips_on_edges |
Source code
|
| place_tips_on_nodes |
Source code
|
| place_tips_taxonomically |
Man page
Source code
|
| place_tips_taxonomically_CPP |
Source code
|
| plot_arc |
Source code
|
| plot_tree_radial |
Man page
Source code
|
| propagate_max_ages_downstream_CPP |
Source code
|
| propagate_min_ages_upstream_CPP |
Source code
|
| random_semiboxed_left |
Source code
|
| rbeta4 |
Source code
|
| read_Newick_string_CPP |
Source code
|
| read_biom_table |
Source code
|
| read_distances_list |
Source code
|
| read_distances_list_CPP |
Source code
|
| read_fasta |
Man page
Source code
|
| read_fasta_from_file_CPP |
Source code
|
| read_fastq |
Man page
Source code
|
| read_fastq_from_file_CPP |
Source code
|
| read_tree |
Man page
Source code
|
| reconstruct_past_diversification |
Man page
Source code
|
| reconstruct_past_diversifications_CPP |
Source code
|
| reconstruct_past_diversity_from_biased_coalescent_CPP |
Source code
|
| reconstruct_past_diversity_from_coalescent_CPP |
Source code
|
| refine_time_grid |
Source code
|
| relative_to_absolute_node_ages_CPP |
Source code
|
| remove_outliers |
Source code
|
| reorder_tree_edges |
Man page
Source code
|
| root_at_midpoint |
Man page
Source code
|
| root_at_node |
Man page
Source code
|
| root_in_edge |
Man page
Source code
|
| root_tree_at_node_CPP |
Source code
|
| root_via_outgroup |
Man page
Source code
|
| root_via_rtt |
Man page
Source code
|
| rowCovs |
Source code
|
| rowVars |
Source code
|
| sample_pairwise_tip_distances |
Source code
|
| sanitize_parameters_for_fitting |
Source code
|
| scale_params |
Source code
|
| shift_clade_times |
Man page
Source code
|
| shift_clade_times_CPP |
Source code
|
| simulate_Ornstein_Uhlenbeck_on_tree_CPP |
Source code
|
| simulate_SBM_on_tree_CPP |
Source code
|
| simulate_SBM_trajectory |
Source code
|
| simulate_SBM_trajectory_CPP |
Source code
|
| simulate_TSBM_on_tree_CPP |
Source code
|
| simulate_bm_model |
Man page
Source code
|
| simulate_deterministic_HBDS_CPP |
Source code
|
| simulate_deterministic_HBD_MSC_CPP |
Source code
|
| simulate_deterministic_HBD_model_CPP |
Source code
|
| simulate_deterministic_diversity_growth_CPP |
Source code
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| simulate_deterministic_hbd |
Man page
Source code
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| simulate_deterministic_hbd_msc |
Source code
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| simulate_deterministic_hbds |
Man page
Source code
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| simulate_diversification_model |
Man page
Source code
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| simulate_dsse |
Man page
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| simulate_fixed_rates_Markov_model_CPP |
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| simulate_geobiased_sbm |
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| simulate_mk_model |
Man page
Source code
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| simulate_multivariate_Brownian_motion_model_CPP |
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| simulate_musse |
Man page
Source code
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| simulate_neutral_gene_evolution |
Source code
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| simulate_neutral_gene_evolution_CPP |
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| simulate_ou_model |
Man page
Source code
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| simulate_reflected_Ornstein_Uhlenbeck_on_tree_CPP |
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| simulate_rou_model |
Man page
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| simulate_sbm |
Man page
Source code
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| simulate_scalar_Brownian_motion_model_CPP |
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| simulate_tdsse |
Man page
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| sliding_window_average1D |
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| smoothenTimeSeriesSavitzkyGolay_CPP |
Source code
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| smoothen_time_series |
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| sort_tree_edges_root_to_tips_CPP |
Source code
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| spline_coefficients |
Man page
Source code
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| split_sphere_into_equisized_tiles |
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| split_tree_at_height |
Man page
Source code
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| split_tree_at_height_CPP |
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| split_undirected_graph_CPP |
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| sprint_tree_parameters |
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| tree_distance |
Man page
Source code
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| tree_from_branching_ages |
Man page
Source code
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| tree_from_placements_CPP |
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| tree_from_sampling_branching_ages |
Man page
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| tree_from_taxa |
Man page
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| tree_from_taxa_file |
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| tree_has_multifurcations_CPP |
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| tree_imbalance |
Man page
Source code
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| tree_to_Newick_string_CPP |
Source code
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| tree_to_clade_list_CPP |
Source code
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| trim_tree_at_height |
Man page
Source code
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| trim_tree_at_height_CPP |
Source code
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| uncompress_musse_params |
Source code
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| unflatten_hbds_params |
Source code
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| unflatten_musse_params |
Source code
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| unlist_with_nulls |
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| unscale_params |
Source code
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| variance |
Source code
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| weighted_graph_Laplacian_of_tree |
Source code
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| write_biom_table |
Source code
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| write_tree |
Man page
Source code
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