Circular Genome Tools
Contents:
cgt package
Circular Genome Tools
»
Index
Index
A
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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R
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S
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T
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U
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W
A
ALGEBRA (class in cgt.enums)
all_adjacent_transpositions_representatives() (in module cgt.rearrangements)
all_inversions (cgt.enums.MODEL attribute)
all_inversions_representatives() (in module cgt.rearrangements)
arrows (cgt.enums.DISPLAY attribute)
C
C_2 (cgt.enums.SYMMETRY attribute)
c_perm() (in module cgt.rearrangements)
canonical_instance() (cgt.position_paradigm.PositionParadigmFramework method)
cgt.distances
module
cgt.enums
module
cgt.examples
module
cgt.genome
module
cgt.hyperoctahedral
module
cgt.models
module
cgt.position_paradigm
module
cgt.rearrangements
module
cgt.simulations
module
cgt.structures
module
cgt.visualisation
module
character_for_tuple() (cgt.hyperoctahedral.hyperoctahedral_group 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)
css() (in module cgt.rearrangements)
cuts() (in module cgt.rearrangements)
cycles (cgt.enums.DISPLAY attribute)
cycles() (cgt.position_paradigm.PositionParadigmFramework method)
D
D_n (cgt.enums.SYMMETRY attribute)
dict_to_distance_matrix() (in module cgt.distances)
dictionary (cgt.enums.FORMAT attribute)
dihedral (cgt.enums.SYMMETRY attribute)
DISPLAY (class in cgt.enums)
DISTANCE (class in cgt.enums)
distance_matrix() (in module cgt.distances)
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
element_in_little_subgroup() (cgt.hyperoctahedral.hyperoctahedral_group method)
equiv_classes (cgt.enums.FORMAT attribute)
evolve_on_tree() (in module cgt.simulations)
example() (in module cgt.examples)
F
flip (cgt.enums.SYMMETRY attribute)
formal_sum (cgt.enums.FORMAT attribute)
FORMAT (class in cgt.enums)
G
genome (cgt.enums.ALGEBRA attribute)
Genome (class in cgt.genome)
genome() (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)
genomes() (cgt.position_paradigm.PositionParadigmFramework method)
group (cgt.enums.ALGEBRA attribute)
group_algebra() (cgt.position_paradigm.PositionParadigmFramework method)
grow_tree() (in module cgt.simulations)
H
hyperoctahedral_group (class in cgt.hyperoctahedral)
hyperoctahedral_twist() (cgt.hyperoctahedral.hyperoctahedral_group method)
HyperoctahedralGroup() (in module cgt.structures)
HyperoctahedralGroupRepresentations() (in module cgt.hyperoctahedral)
I
instances() (cgt.position_paradigm.PositionParadigmFramework method)
irrep() (cgt.hyperoctahedral.hyperoctahedral_group method)
IRREP_TYPE (class in cgt.enums)
irreps() (cgt.position_paradigm.PositionParadigmFramework method)
L
likelihood_function() (in module cgt.distances)
linear (cgt.enums.SYMMETRY attribute)
little_subgroup() (cgt.hyperoctahedral.hyperoctahedral_group method)
little_subgroup_pairs() (cgt.hyperoctahedral.hyperoctahedral_group method)
little_subgroups() (cgt.hyperoctahedral.hyperoctahedral_group method)
M
matrix() (cgt.position_paradigm.PositionParadigmFramework method)
maximise() (in module cgt.distances)
maximum_likelihood_distance (cgt.enums.DISTANCE attribute)
maximum_likelihood_estimate (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_first_passage_time (cgt.enums.DISTANCE attribute)
min_weighted (cgt.enums.DISTANCE attribute)
minimum (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.distances
cgt.enums
cgt.examples
cgt.genome
cgt.hyperoctahedral
cgt.models
cgt.position_paradigm
cgt.rearrangements
cgt.simulations
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_swaps (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.hyperoctahedral_group method)
orthogonal (cgt.enums.IRREP_TYPE attribute)
P
permutation_with_cuts() (in module cgt.rearrangements)
Phi_inv() (cgt.hyperoctahedral.hyperoctahedral_group method)
pos_to_signed_reg (cgt.enums.TYPE attribute)
PositionParadigmFramework (class in cgt.position_paradigm)
R
random_genome() (cgt.position_paradigm.PositionParadigmFramework method)
random_instance() (cgt.position_paradigm.PositionParadigmFramework method)
reflection (cgt.enums.SYMMETRY attribute)
reg_rep() (cgt.models.Model method)
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.hyperoctahedral_group method)
right_transversal() (cgt.hyperoctahedral.hyperoctahedral_group method)
S
S_2 (cgt.enums.SYMMETRY attribute)
s_element() (cgt.models.Model method)
semidirect_product_with_hyperoctahedral_twist() (cgt.hyperoctahedral.hyperoctahedral_group 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_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
two_region_adjacent_transpositions (cgt.enums.MODEL attribute)
two_region_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)