Index A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | R | S | T | U | V | W A add_blur_slider() (cassiopeia.pl.Tree3D method) add_edge_weights() (cassiopeia.solver.ILPSolver method) add_height_key_events() (cassiopeia.pl.Tree3D method) add_height_slider() (cassiopeia.pl.Tree3D method) add_image() (cassiopeia.pl.Tree3D method) add_image_checkboxes() (cassiopeia.pl.Tree3D method) add_leaf() (cassiopeia.data.CassiopeiaTree method) add_node_picking() (cassiopeia.pl.Tree3D method) add_root (cassiopeia.solver.NeighborJoiningSolver attribute) (cassiopeia.solver.UPGMASolver attribute) add_time_slider() (cassiopeia.pl.Tree3D method) add_widgets() (cassiopeia.pl.Tree3D method) align_sequences() (in module cassiopeia.pp) apply_bottom_solver() (cassiopeia.solver.HybridSolver method) apply_top_solver() (cassiopeia.solver.HybridSolver method) assess_cutoff() (cassiopeia.solver.HybridSolver method) B birth_rate (cassiopeia.tl.IIDExponentialBayesian attribute) (cassiopeia.tl.IIDExponentialBayesian property) BirthDeathFitnessSimulator (class in cassiopeia.sim) breadth_first_traverse_edges() (cassiopeia.data.CassiopeiaTree method) BrownianSpatialDataSimulator (class in cassiopeia.sim) C calculate_likelihood_continuous() (in module cassiopeia.tl) calculate_likelihood_discrete() (in module cassiopeia.tl) calculate_parsimony() (in module cassiopeia.tl) call_alleles() (in module cassiopeia.pp) call_lineage_groups() (in module cassiopeia.pp) Cas9LineageTracingDataSimulator (class in cassiopeia.sim) cassiopeia.data module CassiopeiaTree (class in cassiopeia.data) character_matrix (cassiopeia.data.CassiopeiaTree property) children() (cassiopeia.data.CassiopeiaTree method) clear_branch_actors() (cassiopeia.pl.Tree3D method) clear_image_actors() (cassiopeia.pl.Tree3D method) clear_node_actors() (cassiopeia.pl.Tree3D method) clear_picked_mesh() (cassiopeia.pl.Tree3D method) clear_subclone_actor() (cassiopeia.pl.Tree3D method) ClonalSpatialDataSimulator (class in cassiopeia.sim) cluster_dissimilarity() (in module cassiopeia.solver.dissimilarity_functions) collapse_ambiguous_characters() (cassiopeia.data.CassiopeiaTree method) collapse_mutationless_edges() (cassiopeia.data.CassiopeiaTree method) collapse_sites() (cassiopeia.sim.Cas9LineageTracingDataSimulator method) collapse_umis() (in module cassiopeia.pp) collapse_unifurcations() (cassiopeia.data.CassiopeiaTree method) CompleteBinarySimulator (class in cassiopeia.sim) compute_dissimilarity_map() (cassiopeia.data.CassiopeiaTree method) (in module cassiopeia.data) compute_empirical_indel_priors() (in module cassiopeia.pp) compute_evolutionary_coupling() (in module cassiopeia.tl) compute_expansion_pvalues() (in module cassiopeia.tl) compute_morans_i() (in module cassiopeia.tl) compute_phylogenetic_weight_matrix() (in module cassiopeia.data) compute_q() (cassiopeia.solver.NeighborJoiningSolver static method) convert_alleletable_to_character_matrix() (in module cassiopeia.pp) convert_alleletable_to_lineage_profile() (in module cassiopeia.pp) convert_fastqs_to_unmapped_bam() (in module cassiopeia.pp) convert_lineage_profile_to_character_matrix() (in module cassiopeia.pp) copy() (cassiopeia.data.CassiopeiaTree method) create_grid() (cassiopeia.pl.Tree3D method) cut_tree() (cassiopeia.pl.Tree3D method) D depth_first_traverse_edges() (cassiopeia.data.CassiopeiaTree method) depth_first_traverse_nodes() (cassiopeia.data.CassiopeiaTree method) discretization_level (cassiopeia.tl.IIDExponentialBayesian attribute) (cassiopeia.tl.IIDExponentialBayesian property) dissimilarity_function (cassiopeia.solver.NeighborJoiningSolver attribute) (cassiopeia.solver.UPGMASolver attribute) E edges (cassiopeia.data.CassiopeiaTree property) error_correct_cellbcs_to_whitelist() (in module cassiopeia.pp) error_correct_intbcs_to_whitelist() (in module cassiopeia.pp) error_correct_umis() (in module cassiopeia.pp) estimate_branch_lengths() (cassiopeia.tl.IIDExponentialBayesian method) (cassiopeia.tl.IIDExponentialMLE method) estimate_missing_data_rates() (in module cassiopeia.tl) estimate_mutation_rate() (in module cassiopeia.tl) evaluate_cut() (cassiopeia.solver.MaxCutSolver method) F filter_bam() (in module cassiopeia.pp) filter_cells() (in module cassiopeia.pp) filter_molecule_table() (in module cassiopeia.pp) filter_nodes() (cassiopeia.data.CassiopeiaTree method) filter_umis() (in module cassiopeia.pp) find_cherry() (cassiopeia.solver.NeighborJoiningSolver method) (cassiopeia.solver.SharedMutationJoiningSolver method) (cassiopeia.solver.UPGMASolver method) find_lca() (cassiopeia.data.CassiopeiaTree method) find_lcas_of_pairs() (cassiopeia.data.CassiopeiaTree method) fitch_count() (in module cassiopeia.tl) fitch_hartigan() (in module cassiopeia.tl) freeze_character_matrix() (cassiopeia.data.CassiopeiaTree method) G generate_steiner_model() (cassiopeia.solver.ILPSolver method) get_all_ancestors() (cassiopeia.data.CassiopeiaTree method) get_attribute() (cassiopeia.data.CassiopeiaTree method) get_branch_length() (cassiopeia.data.CassiopeiaTree method) get_cassettes() (cassiopeia.sim.Cas9LineageTracingDataSimulator method) get_character_states() (cassiopeia.data.CassiopeiaTree method) get_dissimilarity() (cassiopeia.data.CassiopeiaTree method) get_dissimilarity_map() (cassiopeia.data.CassiopeiaTree method) get_distance() (cassiopeia.data.CassiopeiaTree method) get_distances() (cassiopeia.data.CassiopeiaTree method) get_lca_characters() (in module cassiopeia.data) get_mask() (cassiopeia.pl.Tree3D method) get_max_depth_of_tree() (cassiopeia.data.CassiopeiaTree method) get_mean_depth_of_tree() (cassiopeia.data.CassiopeiaTree method) get_mutations_along_edge() (cassiopeia.data.CassiopeiaTree method) get_newick() (cassiopeia.data.CassiopeiaTree method) get_time() (cassiopeia.data.CassiopeiaTree method) get_times() (cassiopeia.data.CassiopeiaTree method) get_tree_topology() (cassiopeia.data.CassiopeiaTree method) get_unmutated_characters_along_edge() (cassiopeia.data.CassiopeiaTree method) H hamming_distance() (in module cassiopeia.solver.dissimilarity_functions) hamming_similarity_normalized_over_missing() (in module cassiopeia.solver.dissimilarity_functions) hamming_similarity_without_missing() (in module cassiopeia.solver.dissimilarity_functions) HybridSolver (class in cassiopeia.solver) I IIDExponentialBayesian (class in cassiopeia.tl) IIDExponentialMLE (class in cassiopeia.tl) ILPSolver (class in cassiopeia.solver) impute_deducible_missing_states() (cassiopeia.data.CassiopeiaTree method) infer_potential_graph() (cassiopeia.solver.ILPSolver method) init_label_mapping() (cassiopeia.pl.Tree3D method) init_nodes() (cassiopeia.pl.Tree3D method) init_subclones() (cassiopeia.pl.Tree3D method) internal_nodes (cassiopeia.data.CassiopeiaTree property) introduce_states() (cassiopeia.sim.Cas9LineageTracingDataSimulator method) is_ambiguous() (cassiopeia.data.CassiopeiaTree method) is_internal_node() (cassiopeia.data.CassiopeiaTree method) is_leaf() (cassiopeia.data.CassiopeiaTree method) is_root() (cassiopeia.data.CassiopeiaTree method) iterations (cassiopeia.solver.MaxCutSolver attribute) J joining_solver (cassiopeia.solver.PercolationSolver attribute) L labels_from_coordinates() (in module cassiopeia.pl) layers (cassiopeia.data.CassiopeiaTree property) leaves (cassiopeia.data.CassiopeiaTree property) leaves_in_subtree() (cassiopeia.data.CassiopeiaTree method) log_joints() (cassiopeia.tl.IIDExponentialBayesian method) log_likelihood (cassiopeia.tl.IIDExponentialBayesian attribute) (cassiopeia.tl.IIDExponentialBayesian property) (cassiopeia.tl.IIDExponentialMLE attribute) (cassiopeia.tl.IIDExponentialMLE property) M MaxCutGreedySolver (class in cassiopeia.solver) MaxCutSolver (class in cassiopeia.solver) missing_data_classifier (cassiopeia.solver.MaxCutGreedySolver attribute) (cassiopeia.solver.VanillaGreedySolver attribute) module cassiopeia.data mutation_rate (cassiopeia.tl.IIDExponentialBayesian attribute) (cassiopeia.tl.IIDExponentialBayesian property) (cassiopeia.tl.IIDExponentialMLE attribute) (cassiopeia.tl.IIDExponentialMLE property) N n_cell (cassiopeia.data.CassiopeiaTree property) n_character (cassiopeia.data.CassiopeiaTree property) NeighborJoiningSolver (class in cassiopeia.solver) nodes (cassiopeia.data.CassiopeiaTree property) O overlay_data() (cassiopeia.sim.BrownianSpatialDataSimulator method) (cassiopeia.sim.Cas9LineageTracingDataSimulator method) (cassiopeia.sim.ClonalSpatialDataSimulator method) P parameters (cassiopeia.data.CassiopeiaTree property) parent() (cassiopeia.data.CassiopeiaTree method) percolate() (cassiopeia.solver.PercolationSolver method) PercolationSolver (class in cassiopeia.solver) perform_split() (cassiopeia.solver.MaxCutGreedySolver method) (cassiopeia.solver.MaxCutSolver method) (cassiopeia.solver.SpectralGreedySolver method) (cassiopeia.solver.SpectralSolver method) (cassiopeia.solver.VanillaGreedySolver method) place_branches() (cassiopeia.pl.Tree3D method) place_nodes() (cassiopeia.pl.Tree3D method) plot() (cassiopeia.pl.Tree3D method) plot_matplotlib() (in module cassiopeia.pl) plot_plotly() (in module cassiopeia.pl) populate_tree() (cassiopeia.data.CassiopeiaTree method) post_process_steiner_solution() (cassiopeia.solver.ILPSolver method) posterior_time() (cassiopeia.tl.IIDExponentialBayesian method) prior_transformation (cassiopeia.solver.MaxCutGreedySolver attribute) (cassiopeia.solver.MaxCutSolver attribute) (cassiopeia.solver.NeighborJoiningSolver attribute) (cassiopeia.solver.PercolationSolver attribute) (cassiopeia.solver.SharedMutationJoiningSolver attribute) (cassiopeia.solver.SpectralGreedySolver attribute) (cassiopeia.solver.SpectralSolver attribute) (cassiopeia.solver.UPGMASolver attribute) (cassiopeia.solver.VanillaGreedySolver attribute) R reconstruct_ancestral_characters() (cassiopeia.data.CassiopeiaTree method) relabel_nodes() (cassiopeia.data.CassiopeiaTree method) remove_leaves_and_prune_lineages() (cassiopeia.data.CassiopeiaTree method) render_branch() (cassiopeia.pl.Tree3D method) render_node() (cassiopeia.pl.Tree3D method) reorder_children() (cassiopeia.data.CassiopeiaTree method) reset() (cassiopeia.pl.Tree3D method) reset_parameters() (cassiopeia.data.CassiopeiaTree method) reset_selected_node() (cassiopeia.pl.Tree3D method) resolve_ambiguous_characters() (cassiopeia.data.CassiopeiaTree method) resolve_umi_sequence() (in module cassiopeia.pp) robinson_foulds() (in module cassiopeia.critique) root (cassiopeia.data.CassiopeiaTree property) root_tree() (cassiopeia.solver.NeighborJoiningSolver method) (cassiopeia.solver.UPGMASolver method) S sample_bootstrap_allele_tables() (in module cassiopeia.data) sample_bootstrap_character_matrices() (in module cassiopeia.data) sample_lineage_event() (cassiopeia.sim.BirthDeathFitnessSimulator method) sample_points() (cassiopeia.sim.ClonalSpatialDataSimulator method) sampling_probability (cassiopeia.tl.IIDExponentialBayesian attribute) (cassiopeia.tl.IIDExponentialBayesian property) scale_to_unit_length() (cassiopeia.data.CassiopeiaTree method) score_small_parsimony() (in module cassiopeia.tl) sdimension (cassiopeia.solver.MaxCutSolver attribute) select_node() (cassiopeia.pl.Tree3D method) select_node_mesh() (cassiopeia.pl.Tree3D method) set_all_character_states() (cassiopeia.data.CassiopeiaTree method) set_attribute() (cassiopeia.data.CassiopeiaTree method) set_branch_length() (cassiopeia.data.CassiopeiaTree method) set_branch_lengths() (cassiopeia.data.CassiopeiaTree method) set_character_states() (cassiopeia.data.CassiopeiaTree method) set_character_states_at_leaves() (cassiopeia.data.CassiopeiaTree method) set_dissimilarity() (cassiopeia.data.CassiopeiaTree method) set_dissimilarity_map() (cassiopeia.data.CassiopeiaTree method) set_height() (cassiopeia.pl.Tree3D method) set_node_picking() (cassiopeia.pl.Tree3D method) set_root() (cassiopeia.pl.Tree3D method) set_selected_node_as_root() (cassiopeia.pl.Tree3D method) set_shown_image() (cassiopeia.pl.Tree3D method) set_subclone_sigma() (cassiopeia.pl.Tree3D method) set_time() (cassiopeia.data.CassiopeiaTree method) (cassiopeia.pl.Tree3D method) set_times() (cassiopeia.data.CassiopeiaTree method) setup_root_finder() (cassiopeia.solver.NeighborJoiningSolver method) (cassiopeia.solver.UPGMASolver method) SharedMutationJoiningSolver (class in cassiopeia.solver) silence_cassettes() (cassiopeia.sim.Cas9LineageTracingDataSimulator method) similarity_function (cassiopeia.solver.PercolationSolver attribute) (cassiopeia.solver.SharedMutationJoiningSolver attribute) (cassiopeia.solver.SpectralGreedySolver attribute) (cassiopeia.solver.SpectralSolver attribute) SimpleFitSubcloneSimulator (class in cassiopeia.sim) simulate_tree() (cassiopeia.sim.BirthDeathFitnessSimulator method) (cassiopeia.sim.CompleteBinarySimulator method) (cassiopeia.sim.SimpleFitSubcloneSimulator method) solve() (cassiopeia.solver.HybridSolver method) (cassiopeia.solver.ILPSolver method) (cassiopeia.solver.PercolationSolver method) (cassiopeia.solver.SharedMutationJoiningSolver method) solve_steiner_instance() (cassiopeia.solver.ILPSolver method) SpatialLeafSubsampler (class in cassiopeia.sim) SpectralGreedySolver (class in cassiopeia.solver) SpectralSolver (class in cassiopeia.solver) subsample_leaves() (cassiopeia.sim.SpatialLeafSubsampler method) (cassiopeia.sim.SupercellularSampler method) (cassiopeia.sim.UniformLeafSubsampler method) subset_clade() (cassiopeia.data.CassiopeiaTree method) SupercellularSampler (class in cassiopeia.sim) T threshold (cassiopeia.solver.PercolationSolver attribute) (cassiopeia.solver.SpectralGreedySolver attribute) (cassiopeia.solver.SpectralSolver attribute) to_newick() (in module cassiopeia.data) Tree3D (class in cassiopeia.pl) triplets_correct() (in module cassiopeia.critique) U UniformLeafSubsampler (class in cassiopeia.sim) update_actors() (cassiopeia.pl.Tree3D method) update_branches() (cassiopeia.pl.Tree3D method) update_dissimilarity_map() (cassiopeia.solver.NeighborJoiningSolver method) (cassiopeia.solver.UPGMASolver method) update_fitness() (cassiopeia.sim.BirthDeathFitnessSimulator method) update_images() (cassiopeia.pl.Tree3D method) update_similarity_map_and_character_matrix() (cassiopeia.solver.SharedMutationJoiningSolver method) update_subclones() (cassiopeia.pl.Tree3D method) update_texts() (cassiopeia.pl.Tree3D method) UPGMASolver (class in cassiopeia.solver) upload_and_export_itol() (in module cassiopeia.pl) V VanillaGreedySolver (class in cassiopeia.solver) W weighted_hamming_distance() (in module cassiopeia.solver.dissimilarity_functions) weighted_hamming_similarity() (in module cassiopeia.solver.dissimilarity_functions) weights (cassiopeia.solver.SpectralGreedySolver attribute)