Index

A

ALGEBRA (class in cgt.enums) all_adjacent_transpositions_representatives() (in module cgt.rearrangements) all_inversion_instances() (in module cgt.rearrangements) all_inversions (cgt.enums.MODEL attribute)

all_inversions_larger_less_likely (cgt.enums.MODEL attribute) all_inversions_representatives() (in module cgt.rearrangements) all_transposition_instances() (in module cgt.rearrangements) all_transpositions (cgt.enums.MODEL attribute) arrows (cgt.enums.DISPLAY attribute)

C

C_2 (cgt.enums.SYMMETRY attribute) c_perm() (in module cgt.rearrangements) canonical_double_cosets() (cgt.position_paradigm.PositionParadigmFramework method) canonical_instance() (cgt.position_paradigm.PositionParadigmFramework method) cgt.constants module cgt.distances module cgt.enums module cgt.examples module cgt.genome module cgt.hyperoctahedral module cgt.models module cgt.pickle_manager module cgt.position_paradigm module

cgt.rearrangements module cgt.simulations module cgt.sorting module cgt.structures module cgt.visualisation module character_for_tuple() (cgt.hyperoctahedral.HyperoctahedralGroup method) circular (cgt.enums.SYMMETRY attribute) CLASSES (class in cgt.enums) coefficient_in() (cgt.position_paradigm.PositionParadigmFramework method) collect_genome_terms() (cgt.position_paradigm.PositionParadigmFramework method) conjugacy_class() (in module cgt.rearrangements) conjugacy_classes (cgt.enums.CLASSES attribute) cosets (cgt.enums.CLASSES attribute) cut_positions() (in module cgt.rearrangements) cycles (cgt.enums.DISPLAY attribute) cycles() (cgt.position_paradigm.PositionParadigmFramework method)

D

D_n (cgt.enums.SYMMETRY attribute) DATA (class in cgt.enums) dict_to_distance_matrix() (in module cgt.distances) dictionary (cgt.enums.FORMAT attribute) dihedral (cgt.enums.SYMMETRY attribute) discrete_mean_first_passage_time (cgt.enums.DISTANCE attribute) discrete_MFPT (cgt.enums.DISTANCE attribute) discrete_MFPT() (in module cgt.distances) DISPLAY (class in cgt.enums) DISTANCE (class in cgt.enums) distance() (in module cgt.distances)

distance_between() (in module cgt.distances) distance_matrix() (in module cgt.distances) DMFPT (cgt.enums.DISTANCE attribute) double_coset() (in module cgt.rearrangements) double_cosets (cgt.enums.CLASSES attribute) draw_branch_length() (in module cgt.simulations) draw_genome() (in module cgt.simulations) draw_genome_instance() (in module cgt.visualisation) draw_instance() (cgt.position_paradigm.PositionParadigmFramework method) draw_rearrangement() (in module cgt.simulations) draw_tree() (in module cgt.simulations)

E

eig_data (cgt.enums.DATA attribute) eigval_lists (cgt.enums.DATA attribute) eigval_sets (cgt.enums.DATA attribute) eigval_sets_old (cgt.enums.DATA attribute) eigvec_lists (cgt.enums.DATA attribute)

eigvec_mat_inv (cgt.enums.DATA attribute) element_in_little_subgroup() (cgt.hyperoctahedral.HyperoctahedralGroup method) equiv_classes (cgt.enums.FORMAT attribute) evolve_on_tree() (in module cgt.simulations) example() (in module cgt.examples)

F

fast_all_inversion_reps() (in module cgt.rearrangements) fast_canonical_instance_generator() (cgt.position_paradigm.PositionParadigmFramework method) fast_MFPT() (in module cgt.distances) fast_reg_rep_of_zs() (cgt.position_paradigm.PositionParadigmFramework method)

first_nonzero_value() (in module cgt.distances) flip (cgt.enums.SYMMETRY attribute) formal_sum (cgt.enums.FORMAT attribute) FORMAT (class in cgt.enums) Framework (in module cgt.position_paradigm)

G

genome (cgt.enums.ALGEBRA attribute) Genome (class in cgt.genome) genome() (cgt.position_paradigm.PositionParadigmFramework method) genome_canonical_instances() (cgt.position_paradigm.PositionParadigmFramework method) genome_canonical_instances_generator() (cgt.position_paradigm.PositionParadigmFramework method) genome_class (cgt.enums.ALGEBRA attribute) genome_conjugacy_classes() (cgt.position_paradigm.PositionParadigmFramework method) genome_equivalence_classes() (cgt.position_paradigm.PositionParadigmFramework method)

genome_group() (cgt.position_paradigm.PositionParadigmFramework method) GenomeFramework (in module cgt.position_paradigm) genomes() (cgt.position_paradigm.PositionParadigmFramework method) genomes_for_dist_matrix() (in module cgt.distances) get_distance_function() (in module cgt.distances) group (cgt.enums.ALGEBRA attribute) group_algebra() (cgt.position_paradigm.PositionParadigmFramework method) grow_tree() (in module cgt.simulations)

H

hyperoctahedral_twist() (cgt.hyperoctahedral.HyperoctahedralGroup method) HyperoctahedralGroup (class in cgt.hyperoctahedral)

HyperoctahedralGroup() (in module cgt.structures) HyperoctahedralGroupRepresentations() (in module cgt.hyperoctahedral)

I

identity_instance() (cgt.position_paradigm.PositionParadigmFramework method) instances() (cgt.position_paradigm.PositionParadigmFramework method) inversion() (in module cgt.rearrangements) irrep() (cgt.hyperoctahedral.HyperoctahedralGroup method)

IRREP_TYPE (class in cgt.enums) irreps() (cgt.position_paradigm.PositionParadigmFramework method) irreps_z (cgt.enums.DATA attribute) irreps_z_np (cgt.enums.DATA attribute) irreps_zs (cgt.enums.DATA attribute)

L

likelihood_function() (in module cgt.distances) linear (cgt.enums.SYMMETRY attribute)

little_subgroup() (cgt.hyperoctahedral.HyperoctahedralGroup method) little_subgroup_pairs() (cgt.hyperoctahedral.HyperoctahedralGroup method) little_subgroups() (cgt.hyperoctahedral.HyperoctahedralGroup method)

M

maximise() (in module cgt.distances) maximum_likelihood_distance (cgt.enums.DISTANCE attribute) maximum_likelihood_estimate (cgt.enums.DISTANCE attribute) mean_first_passage_time (cgt.enums.DISTANCE attribute) MFPT (cgt.enums.DISTANCE attribute) MFPT() (in module cgt.distances) min (cgt.enums.DISTANCE attribute) min_distance() (in module cgt.distances) min_distance_using_irreps() (in module cgt.distances) min_weighted (cgt.enums.DISTANCE attribute) minimum (cgt.enums.DISTANCE attribute) minimum_distance (cgt.enums.DISTANCE attribute) minimum_weighted (cgt.enums.DISTANCE attribute) MLE (cgt.enums.DISTANCE attribute) mle() (in module cgt.distances) mles() (in module cgt.distances)

MODEL (class in cgt.enums) Model (class in cgt.models) module cgt.constants cgt.distances cgt.enums cgt.examples cgt.genome cgt.hyperoctahedral cgt.models cgt.pickle_manager cgt.position_paradigm cgt.rearrangements cgt.simulations cgt.sorting cgt.structures cgt.visualisation

N

named_model_with_relative_probs() (cgt.models.Model class method)

newick_to_tree() (in module cgt.simulations) num_genomes() (cgt.position_paradigm.PositionParadigmFramework method)

O

one_region_inversions (cgt.enums.MODEL attribute) one_region_moves (cgt.enums.MODEL attribute) one_region_moves_without_inversions (cgt.enums.MODEL attribute) one_row (cgt.enums.DISPLAY attribute) (cgt.enums.SET attribute)

one_row() (cgt.position_paradigm.PositionParadigmFramework method) only_reps (cgt.enums.FORMAT attribute) orbit_representative() (cgt.hyperoctahedral.HyperoctahedralGroup method) orthogonal (cgt.enums.IRREP_TYPE attribute)

P

partial_traces (cgt.enums.DATA attribute) permutation_with_cuts() (in module cgt.rearrangements) Phi() (cgt.hyperoctahedral.HyperoctahedralGroup method) pos_to_signed_reg (cgt.enums.TYPE attribute)

PositionParadigmFramework (class in cgt.position_paradigm) prob_to_reach_in_steps_func() (in module cgt.distances) probability_to_reach_in_steps() (in module cgt.distances) projections (cgt.enums.DATA attribute)

R

random_genome() (cgt.position_paradigm.PositionParadigmFramework method) random_instance() (cgt.position_paradigm.PositionParadigmFramework method) reflection (cgt.enums.SYMMETRY attribute) reg_rep_of_zs (cgt.enums.DATA attribute) reg_rep_of_zs() (cgt.models.Model method) (cgt.position_paradigm.PositionParadigmFramework method)

reg_to_signed_pos (cgt.enums.TYPE attribute) regular_representation() (cgt.position_paradigm.PositionParadigmFramework method) representation_little_subgroup() (cgt.hyperoctahedral.HyperoctahedralGroup method) representatives() (in module cgt.rearrangements) retrieve_irrep_of_z() (in module cgt.pickle_manager) right_transversal() (cgt.hyperoctahedral.HyperoctahedralGroup method) right_transversal_of_little_subgroup() (cgt.hyperoctahedral.HyperoctahedralGroup method)

S

S_2 (cgt.enums.SYMMETRY attribute) s_element() (cgt.models.Model method) segment_length() (in module cgt.rearrangements) segment_midpoint() (in module cgt.rearrangements) semidirect_product_with_hyperoctahedral_twist() (cgt.hyperoctahedral.HyperoctahedralGroup method) seminormal (cgt.enums.IRREP_TYPE attribute) SET (class in cgt.enums) set_node() (in module cgt.simulations) set_plus_minus() (in module cgt.structures) signed_cycles (cgt.enums.SET attribute)

signed_inversion() (in module cgt.rearrangements) signed_pos_to_reg (cgt.enums.TYPE attribute) signed_reg_to_pos (cgt.enums.TYPE attribute) single_coset() (in module cgt.rearrangements) specht (cgt.enums.IRREP_TYPE attribute) speck (cgt.enums.IRREP_TYPE attribute) standard_reflection() (cgt.position_paradigm.PositionParadigmFramework method) standard_rotation() (cgt.position_paradigm.PositionParadigmFramework method) SYMMETRY (class in cgt.enums) symmetry_element() (cgt.position_paradigm.PositionParadigmFramework method) symmetry_group() (cgt.position_paradigm.PositionParadigmFramework method)

T

three_region_transpositions (cgt.enums.MODEL attribute) transposition() (in module cgt.rearrangements) two_region_adjacent_transpositions (cgt.enums.MODEL attribute) two_region_inversions (cgt.enums.MODEL attribute)

two_region_revrevs (cgt.enums.MODEL attribute) two_region_transpositions (cgt.enums.MODEL attribute) two_region_transpositions_without_inversions (cgt.enums.MODEL attribute) TYPE (class in cgt.enums)

U

unsigned_cycles (cgt.enums.SET attribute)

W

wreath (cgt.enums.SET attribute)

wreath_s2 (cgt.enums.SET attribute)