Index

_

__init__() (phylox.cherrypicking.base.CherryPickingMixin method) (phylox.cherrypicking.base.CHERRYTYPE method) (phylox.cherrypicking.combining_networks.HybridizationProblem method) (phylox.classes.networkclass.DiNetworkClass method) (phylox.dinetwork.DiNetwork method) (phylox.generators.trees.add_edges.AddEdgeMethod method) (phylox.rearrangement.exact_distance.base.ExactMethodsMixin method) (phylox.rearrangement.heuristics.green_line_heuristic.HeuristicDistanceMixin method) (phylox.rearrangement.move.Move method) (phylox.rearrangement.movetype.MoveType method) (phylox.rearrangement.rearrangementproblem.RearrangementProblem method)

A

acceptance_probability() (in module phylox.generators.mcmc.base), [1] add_note() (phylox.exceptions.invalidmovedefinitionexception.InvalidMoveDefinitionException method), [1] (phylox.exceptions.invalidmoveexception.InvalidMoveException method), [1] (phylox.exceptions.nosolutionexception.NoSolutionException method), [1] (phylox.exceptions.timeoutexception.TimeoutException method), [1] add_pair() (in module phylox.cherrypicking.base), [1]

add_roots_to_sequence() (in module phylox.cherrypicking.base), [1] AddEdgeMethod (class in phylox.generators.trees.add_edges), [1] all_valid_moves() (in module phylox.rearrangement.move), [1] AllBelow() (in module phylox.rearrangement.heuristics.utils), [1] apply_move() (in module phylox.rearrangement.move), [1] apply_move_sequence() (in module phylox.rearrangement.move), [1] AUTOMORPHISM_LABEL_PREFIX (in module phylox.isomorphism.base), [1]

B

b2_balance() (in module phylox.networkproperties.properties), [1]

blob_properties() (in module phylox.networkproperties.properties), [1]

C

capitalize() (phylox.rearrangement.movetype.MoveType method), [1] casefold() (phylox.rearrangement.movetype.MoveType method), [1] center() (phylox.rearrangement.movetype.MoveType method), [1] check_cherry_picking_sequence() (in module phylox.cherrypicking.tree_child_sequences), [1] check_movable() (in module phylox.rearrangement.movability), [1] check_reducible_pair() (in module phylox.cherrypicking.base), [1] check_solution() (phylox.rearrangement.rearrangementproblem.RearrangementProblem method), [1] check_valid() (in module phylox.rearrangement.movability), [1]

cherry_height() (in module phylox.cherrypicking.base), [1] CherryPickingMixin (class in phylox.cherrypicking.base) CHERRYTYPE (class in phylox.cherrypicking.base), [1] child() (phylox.dinetwork.DiNetwork method), [1] compute_hash() (in module phylox.generators.lgt.base) count() (phylox.rearrangement.movetype.MoveType method), [1] count_automorphisms() (in module phylox.isomorphism.base), [1] count_reducible_pairs() (in module phylox.networkproperties.properties), [1] CPSBound() (phylox.cherrypicking.combining_networks.HybridizationProblem method), [1]

D

DiNetwork (class in phylox.dinetwork), [1]

dinetwork_to_extended_newick() (in module phylox.parser), [1] DiNetworkClass (class in phylox.classes.networkclass), [1]

E

encode() (phylox.rearrangement.movetype.MoveType method), [1] endswith() (phylox.rearrangement.movetype.MoveType method), [1]

ExactMethodsMixin (class in phylox.rearrangement.exact_distance.base) expandtabs() (phylox.rearrangement.movetype.MoveType method), [1] extended_newick_to_dinetwork() (in module phylox.parser), [1]

F

find() (phylox.rearrangement.movetype.MoveType method), [1] Find_All_Pairs() (phylox.cherrypicking.combining_networks.HybridizationProblem method), [1] find_all_reducible_pairs() (in module phylox.cherrypicking.base), [1] find_cherries_with_first() (in module phylox.cherrypicking.base), [1] find_reducible_pairs_with_first() (in module phylox.cherrypicking.base), [1] find_reducible_pairs_with_second() (in module phylox.cherrypicking.base), [1] find_reticulated_cherry_with_first() (in module phylox.cherrypicking.base), [1] find_tree_child_sequence() (in module phylox.cherrypicking.tree_child_sequences), [1]

find_unused_node() (in module phylox.base), [1] FindLeaf() (in module phylox.rearrangement.heuristics.utils) FindRetic() (in module phylox.rearrangement.heuristics.utils) FindTreeNode() (in module phylox.rearrangement.heuristics.utils) format() (phylox.rearrangement.movetype.MoveType method), [1] format_map() (phylox.rearrangement.movetype.MoveType method), [1] from_edge() (in module phylox.rearrangement.invertsequence), [1] from_newick() (phylox.dinetwork.DiNetwork class method), [1]

G

generate_balanced_tree() (in module phylox.generators.trees.well_known), [1] generate_caterpillar() (in module phylox.generators.trees.well_known), [1] generate_network_lgt() (in module phylox.generators.lgt.base) generate_network_random_tree_child_sequence() (in module phylox.generators.randomTC.random_tc_network)

generate_network_zods() (in module phylox.generators.zods.zods) get_indices_of_reducing_pairs() (in module phylox.cherrypicking.base), [1] GL_Case1_Tail() (in module phylox.rearrangement.heuristics.green_line_heuristic) GL_Case3() (in module phylox.rearrangement.heuristics.green_line_heuristic)

H

has_cherry() (in module phylox.cherrypicking.base), [1] Height_Pair() (phylox.cherrypicking.combining_networks.HybridizationProblem method), [1] heuristic_green_line() (phylox.rearrangement.heuristics.green_line_heuristic.HeuristicDistanceMixin method), [1] (phylox.rearrangement.rearrangementproblem.RearrangementProblem method), [1]

heuristic_green_line_random() (phylox.rearrangement.heuristics.green_line_heuristic.HeuristicDistanceMixin method), [1] (phylox.rearrangement.rearrangementproblem.RearrangementProblem method), [1] HeuristicDistanceMixin (class in phylox.rearrangement.heuristics.green_line_heuristic), [1] HighestNodesBelow() (in module phylox.rearrangement.heuristics.utils), [1] HybridizationProblem (class in phylox.cherrypicking.combining_networks), [1]

I

Improve_Sequence() (phylox.cherrypicking.combining_networks.HybridizationProblem method), [1] index() (phylox.rearrangement.movetype.MoveType method), [1] internal_and_external_pairs() (in module phylox.generators.lgt.base) internal_blobs() (in module phylox.generators.lgt.base) InvalidMoveDefinitionException, [1] InvalidMoveException, [1] invert() (phylox.rearrangement.move.Move method), [1] is_binary() (in module phylox.classes.dinetwork), [1] is_isomorphic() (in module phylox.isomorphism.base), [1] is_leaf() (phylox.dinetwork.DiNetwork method), [1] is_leaf_labeled_single_root_network() (in module phylox.classes.dinetwork), [1] is_orchard() (in module phylox.classes.dinetwork), [1] is_reticulation() (phylox.dinetwork.DiNetwork method), [1] is_root() (phylox.dinetwork.DiNetwork method), [1] is_second_in_reducible_pair() (in module phylox.cherrypicking.base) is_stack_free() (in module phylox.classes.dinetwork), [1] is_tree_based() (in module phylox.classes.dinetwork), [1]

is_tree_child() (in module phylox.classes.dinetwork), [1] is_tree_node() (phylox.dinetwork.DiNetwork method), [1] is_type() (phylox.rearrangement.move.Move method), [1] isalnum() (phylox.rearrangement.movetype.MoveType method), [1] isalpha() (phylox.rearrangement.movetype.MoveType method), [1] isascii() (phylox.rearrangement.movetype.MoveType method), [1] isdecimal() (phylox.rearrangement.movetype.MoveType method), [1] isdigit() (phylox.rearrangement.movetype.MoveType method), [1] isidentifier() (phylox.rearrangement.movetype.MoveType method), [1] islower() (phylox.rearrangement.movetype.MoveType method), [1] isnumeric() (phylox.rearrangement.movetype.MoveType method), [1] ISOMETRY_LABEL_ATTR (in module phylox.isomorphism.base), [1] ISOMETRY_LABEL_PREFIX (in module phylox.isomorphism.base), [1] isprintable() (phylox.rearrangement.movetype.MoveType method), [1] isspace() (phylox.rearrangement.movetype.MoveType method), [1] istitle() (phylox.rearrangement.movetype.MoveType method), [1] isupper() (phylox.rearrangement.movetype.MoveType method), [1]

J

join() (phylox.rearrangement.movetype.MoveType method), [1]

L

LABEL_ATTR (in module phylox.constants), [1] label_to_node_dict (phylox.dinetwork.DiNetwork property), [1] labels (phylox.dinetwork.DiNetwork property), [1] last_node() (in module phylox.generators.lgt.base) leaves (phylox.dinetwork.DiNetwork property), [1] leaves() (in module phylox.generators.lgt.base)

LENGTH_ATTR (in module phylox.constants), [1] level() (in module phylox.networkproperties.properties), [1] lgt() (in module phylox.generators.lgt.base) ljust() (phylox.rearrangement.movetype.MoveType method), [1] lower() (phylox.rearrangement.movetype.MoveType method), [1] LowestReticAndTreeNodeAbove() (in module phylox.rearrangement.heuristics.utils), [1] lstrip() (phylox.rearrangement.movetype.MoveType method), [1]

M

maketrans() (phylox.rearrangement.movetype.MoveType static method), [1] module phylox phylox.base phylox.cherrypicking phylox.cherrypicking.base phylox.cherrypicking.best_subnetwork phylox.cherrypicking.combining_networks phylox.cherrypicking.Heuristic_Main_UserFriendly phylox.cherrypicking.tree_child_sequences phylox.classes phylox.classes.dinetwork phylox.classes.networkclass phylox.constants phylox.dinetwork phylox.exceptions phylox.exceptions.invalidmovedefinitionexception phylox.exceptions.invalidmoveexception phylox.exceptions.nosolutionexception phylox.exceptions.timeoutexception phylox.generators phylox.generators.lgt phylox.generators.lgt.base phylox.generators.mcmc phylox.generators.mcmc.base phylox.generators.randomTC phylox.generators.randomTC.random_tc_network phylox.generators.trees phylox.generators.trees.add_edges phylox.generators.trees.beta_splitting_tree phylox.generators.trees.well_known phylox.generators.zods phylox.generators.zods.zods phylox.generators.zods.zods_cli phylox.isomorphism phylox.isomorphism.base phylox.networkproperties phylox.networkproperties.properties phylox.parser phylox.rearrangement phylox.rearrangement.exact_distance phylox.rearrangement.exact_distance.base phylox.rearrangement.heuristics phylox.rearrangement.heuristics.cli_main phylox.rearrangement.heuristics.green_line_heuristic phylox.rearrangement.heuristics.red_line_heuristic phylox.rearrangement.heuristics.utils phylox.rearrangement.invertsequence phylox.rearrangement.movability phylox.rearrangement.move phylox.rearrangement.movetype phylox.rearrangement.rearrangementproblem

Move (class in phylox.rearrangement.move), [1] MoveType (class in phylox.rearrangement.movetype), [1] multree_to_dinetwork() (in module phylox.generators.zods.zods), [1]

N

network_from_tree() (in module phylox.generators.trees.add_edges)

newick() (phylox.dinetwork.DiNetwork method), [1] NoSolutionException, [1]

P

parent() (phylox.dinetwork.DiNetwork method), [1] partition() (phylox.rearrangement.movetype.MoveType method), [1] phylox module phylox.base module phylox.cherrypicking module phylox.cherrypicking.base module phylox.cherrypicking.best_subnetwork module phylox.cherrypicking.combining_networks module phylox.cherrypicking.Heuristic_Main_UserFriendly module phylox.cherrypicking.tree_child_sequences module phylox.classes module phylox.classes.dinetwork module phylox.classes.networkclass module phylox.constants module phylox.dinetwork module phylox.exceptions module phylox.exceptions.invalidmovedefinitionexception module phylox.exceptions.invalidmoveexception module phylox.exceptions.nosolutionexception module phylox.exceptions.timeoutexception module phylox.generators module phylox.generators.lgt module phylox.generators.lgt.base module phylox.generators.mcmc module phylox.generators.mcmc.base module phylox.generators.randomTC module phylox.generators.randomTC.random_tc_network module

phylox.generators.trees module phylox.generators.trees.add_edges module phylox.generators.trees.beta_splitting_tree module phylox.generators.trees.well_known module phylox.generators.zods module phylox.generators.zods.zods module phylox.generators.zods.zods_cli module phylox.isomorphism module phylox.isomorphism.base module phylox.networkproperties module phylox.networkproperties.properties module phylox.parser module phylox.rearrangement module phylox.rearrangement.exact_distance module phylox.rearrangement.exact_distance.base module phylox.rearrangement.heuristics module phylox.rearrangement.heuristics.cli_main module phylox.rearrangement.heuristics.green_line_heuristic module phylox.rearrangement.heuristics.red_line_heuristic module phylox.rearrangement.heuristics.utils module phylox.rearrangement.invertsequence module phylox.rearrangement.movability module phylox.rearrangement.move module phylox.rearrangement.movetype module phylox.rearrangement.rearrangementproblem module

R

random_move() (phylox.rearrangement.move.Move class method), [1] random_tree_child_sequence() (in module phylox.generators.randomTC.random_tc_network) random_tree_child_subsequence() (in module phylox.generators.randomTC.random_tc_network) random_vplu_move_at_bottom() (in module phylox.generators.trees.add_edges) random_vplu_move_local() (in module phylox.generators.trees.add_edges) random_vplu_move_uniform() (in module phylox.generators.trees.add_edges) RearrangementProblem (class in phylox.rearrangement.rearrangementproblem), [1] reduce_pair() (in module phylox.cherrypicking.base), [1] Reduce_Pair_In_All() (phylox.cherrypicking.combining_networks.HybridizationProblem method), [1] Reduce_Trivial_Pairs() (phylox.cherrypicking.combining_networks.HybridizationProblem method), [1] Reduce_Trivial_Pairs_Lengths() (phylox.cherrypicking.combining_networks.HybridizationProblem method), [1] Reduce_Trivial_Pairs_Store_Pairs() (phylox.cherrypicking.combining_networks.HybridizationProblem method), [1] remove_unlabeled_leaves() (in module phylox.base), [1] removeprefix() (phylox.rearrangement.movetype.MoveType method), [1]

removesuffix() (phylox.rearrangement.movetype.MoveType method), [1] rename_nodes() (phylox.rearrangement.move.Move method), [1] replace() (phylox.rearrangement.movetype.MoveType method), [1] RETIC_PREFIX (in module phylox.constants), [1] reticulation_number (phylox.dinetwork.DiNetwork property), [1] reticulations (phylox.dinetwork.DiNetwork property), [1] reticulations() (in module phylox.generators.lgt.base) rfind() (phylox.rearrangement.movetype.MoveType method), [1] rindex() (phylox.rearrangement.movetype.MoveType method), [1] rjust() (phylox.rearrangement.movetype.MoveType method), [1] roots (phylox.dinetwork.DiNetwork property), [1] rpartition() (phylox.rearrangement.movetype.MoveType method), [1] rsplit() (phylox.rearrangement.movetype.MoveType method), [1] rstrip() (phylox.rearrangement.movetype.MoveType method), [1]

S

sample_mcmc_networks() (in module phylox.generators.mcmc.base) simulate_beta_splitting() (in module phylox.generators.trees.beta_splitting_tree) simulation_3() (in module phylox.generators.lgt.base) solve_depth_first() (phylox.rearrangement.exact_distance.base.ExactMethodsMixin method) (phylox.rearrangement.rearrangementproblem.RearrangementProblem method), [1] solve_depth_first_bounded() (phylox.rearrangement.exact_distance.base.ExactMethodsMixin method) (phylox.rearrangement.rearrangementproblem.RearrangementProblem method), [1]

speciate() (in module phylox.generators.lgt.base) split() (phylox.rearrangement.movetype.MoveType method), [1] splitlines() (phylox.rearrangement.movetype.MoveType method), [1] startswith() (phylox.rearrangement.movetype.MoveType method), [1] strip() (phylox.rearrangement.movetype.MoveType method), [1] suppress_node() (in module phylox.base), [1] swapcase() (phylox.rearrangement.movetype.MoveType method), [1]

T

TimeoutException, [1] title() (phylox.rearrangement.movetype.MoveType method), [1]

translate() (phylox.rearrangement.movetype.MoveType method), [1] tree_child_network_contains() (in module phylox.cherrypicking.tree_child_sequences), [1] Trivial_Pair_With() (phylox.cherrypicking.combining_networks.HybridizationProblem method), [1]

U

Update_Heights() (phylox.cherrypicking.combining_networks.HybridizationProblem method), [1]

Update_Reducible_Pairs() (phylox.cherrypicking.combining_networks.HybridizationProblem method), [1] upper() (phylox.rearrangement.movetype.MoveType method), [1]

W

with_traceback() (phylox.exceptions.invalidmovedefinitionexception.InvalidMoveDefinitionException method), [1] (phylox.exceptions.invalidmoveexception.InvalidMoveException method), [1] (phylox.exceptions.nosolutionexception.NoSolutionException method), [1] (phylox.exceptions.timeoutexception.TimeoutException method), [1]

Z

zfill() (phylox.rearrangement.movetype.MoveType method), [1]