Index

A

add_edge_weights() (cassiopeia.solver.ILPSolver method) add_leaf() (cassiopeia.data.CassiopeiaTree method) add_root (cassiopeia.solver.NeighborJoiningSolver attribute) (cassiopeia.solver.UPGMASolver attribute)

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

BirthDeathFitnessSimulator (class in cassiopeia.sim)

C

call_alleles() (in module cassiopeia.pp) call_lineage_groups() (in module cassiopeia.pp) Cas9LineageTracingDataSimulator (class in cassiopeia.sim) cassiopeia.data module cassiopeia.pl module cassiopeia.pp module cassiopeia.sim module cassiopeia.solver module CassiopeiaTree (class in cassiopeia.data) character_matrix (cassiopeia.data.CassiopeiaTree property)

children() (cassiopeia.data.CassiopeiaTree method) 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_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)

D

depth_first_traverse_edges() (cassiopeia.data.CassiopeiaTree method) depth_first_traverse_nodes() (cassiopeia.data.CassiopeiaTree method)

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) 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) 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_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)

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

ILPSolver (class in cassiopeia.solver) infer_potential_graph() (cassiopeia.solver.ILPSolver 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

layers (cassiopeia.data.CassiopeiaTree property)

leaves (cassiopeia.data.CassiopeiaTree property) leaves_in_subtree() (cassiopeia.data.CassiopeiaTree method)

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 cassiopeia.pl cassiopeia.pp cassiopeia.sim cassiopeia.solver

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.Cas9LineageTracingDataSimulator method)

P

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) populate_tree() (cassiopeia.data.CassiopeiaTree method)

post_process_steiner_solution() (cassiopeia.solver.ILPSolver 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_leaf_and_prune_lineage() (cassiopeia.data.CassiopeiaTree method) resolve_ambiguous_characters() (cassiopeia.data.CassiopeiaTree method)

resolve_umi_sequence() (in module cassiopeia.pp) 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) sdimension (cassiopeia.solver.MaxCutSolver attribute) 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_time() (cassiopeia.data.CassiopeiaTree 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) SpectralGreedySolver (class in cassiopeia.solver) SpectralSolver (class in cassiopeia.solver) subsample_leaves() (cassiopeia.sim.SupercellularSampler method) (cassiopeia.sim.UniformLeafSubsampler 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)

U

UniformLeafSubsampler (class in cassiopeia.sim) update_dissimilarity_map() (cassiopeia.solver.NeighborJoiningSolver method) (cassiopeia.solver.UPGMASolver method)

update_fitness() (cassiopeia.sim.BirthDeathFitnessSimulator method) update_similarity_map_and_character_matrix() (cassiopeia.solver.SharedMutationJoiningSolver 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)