alifestd_calc_polytomic_index()
AlifestdIplotxShimNumpy
AlifestdIplotxShimPandas
AlifestdIplotxShimPolars
alifestd_add_global_root()
alifestd_add_global_root_polars()
alifestd_add_inner_knuckles_asexual()
alifestd_add_inner_knuckles_polars()
alifestd_add_inner_leaves()
alifestd_add_inner_niblings_asexual()
alifestd_add_inner_niblings_polars()
alifestd_aggregate_phylogenies()
alifestd_aggregate_phylogenies_polars()
alifestd_as_newick_asexual()
alifestd_as_newick_polars()
alifestd_assign_contiguous_ids()
alifestd_assign_contiguous_ids_polars()
alifestd_assign_root_ancestor_token()
alifestd_calc_clade_lookback_n_asexual()
alifestd_calc_clade_lookback_origin_time_delta_asexual()
alifestd_calc_clade_trait_count_asexual()
alifestd_calc_clade_trait_frequency_asexual()
alifestd_calc_distance_matrix_asexual()
alifestd_calc_distance_matrix_polars()
alifestd_calc_mrca_id_matrix_asexual()
alifestd_calc_mrca_id_matrix_asexual_polars()
alifestd_calc_mrca_id_vector_asexual()
alifestd_calc_mrca_id_vector_asexual_polars()
alifestd_calc_polytomic_index_polars()
alifestd_categorize_triplet_asexual()
alifestd_check_topological_sensitivity()
alifestd_check_topological_sensitivity_polars()
alifestd_chronological_sort()
alifestd_chronological_sort_polars()
alifestd_coarsen_dilate_asexual()
alifestd_coarsen_dilate_polars()
alifestd_coarsen_mask()
alifestd_coarsen_taxa_asexual()
alifestd_coarsen_taxa_asexual_make_agg()
alifestd_coerce_chronological_consistency()
alifestd_collapse_trunk_asexual()
alifestd_collapse_trunk_polars()
alifestd_collapse_unifurcations()
alifestd_collapse_unifurcations_polars()
alifestd_convert_root_ancestor_token()
alifestd_count_children_of_asexual()
alifestd_count_children_of_polars()
alifestd_count_inner_nodes()
alifestd_count_inner_nodes_polars()
alifestd_count_leaf_nodes()
alifestd_count_leaf_nodes_polars()
alifestd_count_polytomies()
alifestd_count_polytomies_polars()
alifestd_count_root_nodes()
alifestd_count_root_nodes_polars()
alifestd_count_unifurcating_roots_asexual()
alifestd_count_unifurcating_roots_polars()
alifestd_count_unifurcations()
alifestd_count_unifurcations_polars()
alifestd_delete_trunk_asexual()
alifestd_delete_trunk_asexual_polars()
alifestd_delete_unifurcating_roots_asexual()
alifestd_delete_unifurcating_roots_polars()
alifestd_downsample_tips_asexual()
alifestd_downsample_tips_canopy_asexual()
alifestd_downsample_tips_canopy_polars()
alifestd_downsample_tips_clade_asexual()
alifestd_downsample_tips_clade_polars()
alifestd_downsample_tips_lineage_asexual()
alifestd_downsample_tips_lineage_polars()
alifestd_downsample_tips_lineage_stratified_asexual()
alifestd_downsample_tips_lineage_stratified_polars()
alifestd_downsample_tips_polars()
alifestd_downsample_tips_uniform_asexual()
alifestd_downsample_tips_uniform_polars()
alifestd_drop_topological_sensitivity()
alifestd_drop_topological_sensitivity_polars()
alifestd_estimate_triplet_distance_asexual()
alifestd_find_chronological_inconsistency()
alifestd_find_chronological_inconsistency_polars()
alifestd_find_leaf_ids()
alifestd_find_leaf_ids_polars()
alifestd_find_mrca_id_asexual()
alifestd_find_pair_distance_asexual()
alifestd_find_pair_distance_polars()
alifestd_find_pair_mrca_id_asexual()
alifestd_find_pair_mrca_id_polars()
alifestd_find_root_ids()
alifestd_find_root_ids_polars()
alifestd_from_avida_spop()
alifestd_from_avida_spop_polars()
alifestd_from_newick()
alifestd_from_newick_polars()
alifestd_has_compact_ids()
alifestd_has_compact_ids_polars()
alifestd_has_contiguous_ids()
alifestd_has_contiguous_ids_polars()
alifestd_has_increasing_ids()
alifestd_has_increasing_ids_polars()
alifestd_has_multiple_roots()
alifestd_has_multiple_roots_polars()
alifestd_is_asexual()
alifestd_is_asexual_polars()
alifestd_is_chronologically_ordered()
alifestd_is_chronologically_ordered_polars()
alifestd_is_chronologically_sorted()
alifestd_is_chronologically_sorted_polars()
alifestd_is_sexual()
alifestd_is_sexual_polars()
alifestd_is_strictly_bifurcating_asexual()
alifestd_is_strictly_bifurcating_polars()
alifestd_is_topologically_sorted()
alifestd_is_topologically_sorted_polars()
alifestd_is_ultrametric()
alifestd_is_ultrametric_polars()
alifestd_is_working_format_asexual()
alifestd_is_working_format_polars()
alifestd_join_roots()
alifestd_join_roots_polars()
alifestd_ladderize_asexual()
alifestd_ladderize_polars()
alifestd_make_ancestor_id_col()
alifestd_make_ancestor_id_col_polars()
alifestd_make_ancestor_list_col()
alifestd_make_ancestor_list_col_polars()
alifestd_make_balanced_bifurcating()
alifestd_make_balanced_bifurcating_polars()
alifestd_make_comb()
alifestd_make_comb_polars()
alifestd_make_edge_split()
alifestd_make_edge_split_polars()
alifestd_make_empty()
alifestd_make_empty_polars()
alifestd_make_leaf_split()
alifestd_make_leaf_split_polars()
alifestd_make_star()
alifestd_make_star_polars()
alifestd_mark_ancestor_origin_time_asexual()
alifestd_mark_ancestor_origin_time_polars()
alifestd_mark_clade_duration_asexual()
alifestd_mark_clade_duration_polars()
alifestd_mark_clade_duration_ratio_sister_asexual()
alifestd_mark_clade_duration_ratio_sister_polars()
alifestd_mark_clade_faithpd_asexual()
alifestd_mark_clade_faithpd_polars()
alifestd_mark_clade_fblr_growth_children_asexual()
alifestd_mark_clade_fblr_growth_sister_asexual()
alifestd_mark_clade_leafcount_ratio_sister_asexual()
alifestd_mark_clade_leafcount_ratio_sister_polars()
alifestd_mark_clade_logistic_growth_children_asexual()
alifestd_mark_clade_logistic_growth_sister_asexual()
alifestd_mark_clade_nodecount_ratio_sister_asexual()
alifestd_mark_clade_nodecount_ratio_sister_polars()
alifestd_mark_clade_subtended_duration_asexual()
alifestd_mark_clade_subtended_duration_polars()
alifestd_mark_clade_subtended_duration_ratio_sister_asexual()
alifestd_mark_clade_subtended_duration_ratio_sister_polars()
alifestd_mark_colless_index_asexual()
alifestd_mark_colless_index_corrected_asexual()
alifestd_mark_colless_index_corrected_polars()
alifestd_mark_colless_index_polars()
alifestd_mark_colless_like_index_mdm_asexual()
alifestd_mark_colless_like_index_mdm_polars()
alifestd_mark_colless_like_index_sd_asexual()
alifestd_mark_colless_like_index_sd_polars()
alifestd_mark_colless_like_index_var_asexual()
alifestd_mark_colless_like_index_var_polars()
alifestd_mark_csr_children_asexual()
alifestd_mark_csr_children_polars()
alifestd_mark_csr_offsets_asexual()
alifestd_mark_csr_offsets_polars()
alifestd_mark_first_child_id_asexual()
alifestd_mark_first_child_id_polars()
alifestd_mark_is_left_child_asexual()
alifestd_mark_is_left_child_polars()
alifestd_mark_is_right_child_asexual()
alifestd_mark_is_right_child_polars()
alifestd_mark_leaves()
alifestd_mark_leaves_polars()
alifestd_mark_left_child_asexual()
alifestd_mark_left_child_polars()
alifestd_mark_lineage_cummax_asexual()
alifestd_mark_lineage_cummax_polars()
alifestd_mark_lineage_cummin_asexual()
alifestd_mark_lineage_cummin_polars()
alifestd_mark_lineage_cumprod_asexual()
alifestd_mark_lineage_cumprod_polars()
alifestd_mark_lineage_cumsum_asexual()
alifestd_mark_lineage_cumsum_polars()
alifestd_mark_max_descendant_origin_time_asexual()
alifestd_mark_max_descendant_origin_time_polars()
alifestd_mark_next_sibling_id_asexual()
alifestd_mark_next_sibling_id_polars()
alifestd_mark_node_depth_asexual()
alifestd_mark_node_depth_polars()
alifestd_mark_num_children_asexual()
alifestd_mark_num_children_polars()
alifestd_mark_num_descendants_asexual()
alifestd_mark_num_descendants_polars()
alifestd_mark_num_leaves_asexual()
alifestd_mark_num_leaves_polars()
alifestd_mark_num_leaves_sibling_asexual()
alifestd_mark_num_leaves_sibling_polars()
alifestd_mark_num_preceding_leaves_asexual()
alifestd_mark_num_preceding_leaves_polars()
alifestd_mark_oldest_root()
alifestd_mark_oldest_root_polars()
alifestd_mark_origin_time_delta_asexual()
alifestd_mark_origin_time_delta_polars()
alifestd_mark_ot_mrca_asexual()
alifestd_mark_ot_mrca_polars()
alifestd_mark_prev_sibling_id_asexual()
alifestd_mark_prev_sibling_id_polars()
alifestd_mark_right_child_asexual()
alifestd_mark_right_child_polars()
alifestd_mark_root_id()
alifestd_mark_root_id_polars()
alifestd_mark_roots()
alifestd_mark_roots_polars()
alifestd_mark_sackin_index_asexual()
alifestd_mark_sackin_index_polars()
alifestd_mark_sample_tips_asexual()
alifestd_mark_sample_tips_canopy_asexual()
alifestd_mark_sample_tips_canopy_polars()
alifestd_mark_sample_tips_clade_asexual()
alifestd_mark_sample_tips_clade_polars()
alifestd_mark_sample_tips_lineage_asexual()
alifestd_mark_sample_tips_lineage_polars()
alifestd_mark_sample_tips_lineage_stratified_asexual()
alifestd_mark_sample_tips_lineage_stratified_polars()
alifestd_mark_sample_tips_polars()
alifestd_mark_sample_tips_uniform_asexual()
alifestd_mark_sample_tips_uniform_polars()
alifestd_mark_sister_asexual()
alifestd_mark_sister_polars()
alifestd_mask_descendants_asexual()
alifestd_mask_descendants_polars()
alifestd_mask_monomorphic_clades_asexual()
alifestd_parse_ancestor_id()
alifestd_parse_ancestor_ids()
alifestd_pipe_unary_ops()
alifestd_pipe_unary_ops_polars()
alifestd_prefix_roots()
alifestd_prefix_roots_polars()
alifestd_prune_extinct_lineages_asexual()
alifestd_prune_extinct_lineages_polars()
alifestd_reroot_at_id_asexual()
alifestd_reroot_at_id_polars()
alifestd_sample_triplet_comparisons_asexual()
alifestd_screen_trait_defined_clades_fisher_asexual()
alifestd_screen_trait_defined_clades_fitch_asexual()
alifestd_screen_trait_defined_clades_naive_asexual()
alifestd_sort_children_asexual()
alifestd_sort_children_polars()
alifestd_splay_polytomies()
alifestd_splay_polytomies_polars()
alifestd_sum_origin_time_deltas_asexual()
alifestd_sum_origin_time_deltas_polars()
alifestd_test_leaves_isomorphic_asexual()
alifestd_test_leaves_isomorphic_polars()
alifestd_to_iplotx_pandas()
alifestd_to_iplotx_polars()
alifestd_to_working_format()
alifestd_to_working_format_polars()
alifestd_topological_sensitivity_warned()
alifestd_topological_sensitivity_warned_polars()
alifestd_topological_sort()
alifestd_topological_sort_polars()
alifestd_try_add_ancestor_id_col()
alifestd_try_add_ancestor_id_col_polars()
alifestd_try_add_ancestor_list_col()
alifestd_try_add_ancestor_list_col_polars()
alifestd_ultrametricize()
alifestd_ultrametricize_polars()
alifestd_unfurl_lineage_asexual()
alifestd_unfurl_traversal_inorder_asexual()
alifestd_unfurl_traversal_inorder_polars()
alifestd_unfurl_traversal_levelorder_asexual()
alifestd_unfurl_traversal_levelorder_polars()
alifestd_unfurl_traversal_postorder_asexual()
alifestd_unfurl_traversal_postorder_contiguous_asexual()
alifestd_unfurl_traversal_postorder_contiguous_polars()
alifestd_unfurl_traversal_postorder_polars()
alifestd_unfurl_traversal_preorder_asexual()
alifestd_unfurl_traversal_preorder_polars()
alifestd_unfurl_traversal_semiorder_asexual()
alifestd_unfurl_traversal_semiorder_polars()
alifestd_unfurl_traversal_topological_asexual()
alifestd_unfurl_traversal_topological_polars()
alifestd_validate()
alifestd_warn_topological_sensitivity()
alifestd_warn_topological_sensitivity_polars()
Count how many fewer inner nodes are contained in phylogeny than expected if strictly bifurcationg.
Excludes unifurcations from calculation.