Tandem Repeat Annotation Library
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A
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B
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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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K
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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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V
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W
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X
A
alphabet (tral.hmm.hmm.HMM attribute)
attribute() (in module tral.repeat_list.repeat_list)
B
BinaryExecutable (class in tral.sequence.repeat_detection_run)
C
calc_index_msa() (tral.repeat.repeat.Repeat method)
calc_n_effective() (tral.repeat.repeat.Repeat method)
calc_pvalues() (in module tral.repeat.repeat_pvalue)
calculate_log10_indel_probability() (in module tral.hmm.hmm_own_model)
calculate_log10_probability_indel_lengths() (in module tral.hmm.hmm_own_model)
calculate_MAP_Indel_length_exponential_factor() (in module tral.hmm.hmm_own_model)
calculate_MAP_Indel_length_Zipfian_factor() (in module tral.hmm.hmm_own_model)
calculate_MAP_indel_rate() (in module tral.hmm.hmm_own_model)
calculate_pdf_scores() (in module tral.repeat.repeat_score)
calculate_position_in_alignment() (in module tral.repeat.repeat)
calculate_pvalues() (tral.repeat.repeat.Repeat method)
calculate_repeat_structure() (in module tral.repeat.repeat_pvalue)
calculate_scores() (tral.repeat.repeat.Repeat method)
check_java_errors() (in module tral.sequence.repeat_detection_run)
cluster() (tral.repeat_list.repeat_list.RepeatList method)
column_pdf() (in module tral.repeat.repeat_pvalue)
common_ancestry() (in module tral.repeat_list.repeat_list)
count_repeats() (in module tral.search.filter_hmm)
create() (tral.hmm.hmm.HMM static method)
(tral.repeat.repeat.Repeat method)
(tral.repeat_list.repeat_list.RepeatList method)
(tral.sequence.sequence.Sequence method)
create_from_repeat() (tral.hmm.hmm.HMM static method)
D
d_average_multinom() (in module tral.repeat.repeat_pvalue)
d_average_multiple_max_multinom() (in module tral.repeat.repeat_pvalue)
d_average_multiple_pars_multinom() (in module tral.repeat.repeat_pvalue)
delete_insertion_columns() (tral.repeat.repeat.Repeat method)
derivative_log_posterior() (in module tral.hmm.hmm_own_model)
detect() (tral.sequence.sequence.Sequence method)
Detectors() (in module tral.sequence.repeat_detection_run)
distance_index() (in module tral.hmm.hmm_viterbi)
divergence() (in module tral.repeat_list.repeat_list)
divergence_from_FP_simulations() (in module tral.hmm.hmm_own_model)
E
empirical_list() (in module tral.repeat.repeat_pvalue)
entropy() (in module tral.repeat.repeat_score)
evolved_tandem_repeats() (in module tral.repeat.repeat_io)
F
filter() (tral.repeat_list.repeat_list.RepeatList method)
filter_fasta() (in module tral.search.filter_hmm)
filter_search_results() (in module tral.search.filter_hmm)
G
gap_penalty() (in module tral.repeat.repeat_pvalue)
gap_structure() (tral.repeat.repeat.Repeat method)
gap_structure_HMM() (tral.repeat.repeat.Repeat method)
get_direct_transition_probabilities_for_deletions() (tral.hmm.hmm.HMM method)
get_execute_line() (tral.sequence.repeat_detection_run.BinaryExecutable method)
get_execute_tokens() (tral.sequence.repeat_detection_run.BinaryExecutable method)
get_exon_measures() (in module tral.repeat.repeat_exon)
get_exon_structure() (in module tral.repeat.repeat_exon)
get_repeatlist() (tral.sequence.sequence.Sequence method)
getMSA() (in module tral.sequence.repeat_detection_io)
H
hhpredid_get_repeats() (in module tral.sequence.repeat_detection_io)
HMM (class in tral.hmm.hmm)
(class in tral.hmm.hmm_own_model)
hmm_example() (tral.hmm.hmm.HMM method)
HMM_from_file() (tral.hmm.hmm_own_model.HMM method)
HMM_from_TR() (tral.hmm.hmm_own_model.HMM method)
HMM_from_TR_One_step() (tral.hmm.hmm_own_model.HMM method)
hmm_path_to_aligned_tandem_repeat_units() (in module tral.hmm.hmm_viterbi)
hmm_path_to_maximal_complete_tandem_repeat_units() (in module tral.hmm.hmm_viterbi)
hmm_path_to_non_aligned_tandem_repeat_units() (in module tral.hmm.hmm_viterbi)
hmmer (tral.hmm.hmm.HMM attribute)
hmmer3_emission_probabilities() (in module tral.hmm.hmm)
(in module tral.hmm.hmm_own_model)
I
id (tral.hmm.hmm.HMM attribute)
initialise_HMM_structure() (tral.hmm.hmm.HMM method)
(tral.hmm.hmm_own_model.HMM method)
insertion_states (tral.hmm.hmm.HMM attribute)
K
K80() (in module tral.repeat.repeat_score)
L
l_effective (tral.hmm.hmm.HMM attribute)
(tral.repeat.repeat.Repeat attribute)
l_msa (tral.repeat.repeat.Repeat attribute)
LG() (in module tral.repeat.repeat_score)
load_equilibrium_freq() (in module tral.repeat.repeat_score)
logger (in module tral.repeat.repeat_exon)
loglikelihood_gaps_starphylogeny_zipfian() (in module tral.repeat.repeat_score)
loglikelihood_substitution() (in module tral.hmm.hmm_own_model)
(in module tral.repeat.repeat_score)
logodds() (in module tral.hmm.hmm_viterbi)
M
main() (in module tral.search.filter_hmm)
(in module tral.search.search_hmm)
match_seqs() (in module tral.search.filter_hmm)
match_states (tral.hmm.hmm.HMM attribute)
mean_similarity() (in module tral.repeat.repeat_score)
module
tral.hmm.hmm
tral.hmm.hmm_io
tral.hmm.hmm_own_model
tral.hmm.hmm_viterbi
tral.repeat.repeat
tral.repeat.repeat_align
tral.repeat.repeat_exon
tral.repeat.repeat_io
tral.repeat.repeat_pvalue
tral.repeat.repeat_score
tral.repeat_list.repeat_list
tral.repeat_list.repeat_list_io
tral.search.filter_hmm
tral.search.search_hmm
tral.sequence.repeat_detection_io
tral.sequence.repeat_detection_run
tral.sequence.sequence
tral.sequence.sequence_io
msa (tral.repeat.repeat.Repeat attribute)
msa_original (tral.repeat.repeat.Repeat attribute)
msaT (tral.repeat.repeat.Repeat attribute)
N
n (tral.repeat.repeat.Repeat attribute)
n_effective (tral.repeat.repeat.Repeat attribute)
n_gaps (tral.repeat.repeat.Repeat attribute)
none_overlapping() (in module tral.repeat_list.repeat_list)
none_overlapping_fixed_repeats() (in module tral.repeat_list.repeat_list)
O
opengzip() (in module tral.search.search_hmm)
optimisation() (in module tral.repeat.repeat_score)
P
p_0 (tral.hmm.hmm.HMM attribute)
p_e (tral.hmm.hmm.HMM attribute)
p_t (tral.hmm.hmm.HMM attribute)
parse_hits() (in module tral.search.filter_hmm)
parse_line() (tral.search.search_hmm.TralHit class method)
parsimony() (in module tral.repeat.repeat_score)
phobos_get_repeats() (in module tral.sequence.repeat_detection_io)
print_exon_structure() (in module tral.repeat.repeat_exon)
probability_of_the_former_state() (in module tral.hmm.hmm_viterbi)
pSim() (in module tral.repeat.repeat_score)
pvalue() (in module tral.repeat_list.repeat_list)
pvalue_from_empirical_list() (in module tral.repeat.repeat_pvalue)
pvalue_pars() (in module tral.repeat.repeat_pvalue)
pvalue_psim() (in module tral.repeat.repeat_pvalue)
R
random_sequence() (in module tral.repeat.repeat_io)
read() (in module tral.hmm.hmm_io)
(tral.hmm.hmm.HMM static method)
read_fasta() (in module tral.repeat.repeat_io)
(in module tral.sequence.sequence_io)
read_HMMER_acc_lengths() (in module tral.hmm.hmm_io)
realign_repeat() (in module tral.repeat.repeat_align)
realign_TR() (tral.repeat.repeat.Repeat method)
remove_char() (in module tral.repeat.repeat_align)
remove_gaps() (in module tral.repeat.repeat_align)
Repeat (class in tral.repeat.repeat)
repeat_in_sequence() (tral.sequence.sequence.Sequence method)
repeat_region_length (tral.repeat.repeat.Repeat attribute)
RepeatList (class in tral.repeat_list.repeat_list)
repeats (tral.repeat_list.repeat_list.RepeatList attribute)
run_detector() (in module tral.sequence.repeat_detection_run)
S
save_original_msa() (tral.repeat.repeat.Repeat method)
save_repeat_fasta() (in module tral.repeat.repeat_io)
save_repeat_stockholm() (in module tral.repeat.repeat_io)
save_repeat_treks() (in module tral.repeat.repeat_io)
seq (tral.sequence.sequence.Sequence attribute)
seq_standard_aa (tral.sequence.sequence.Sequence attribute)
Sequence (class in tral.sequence.sequence)
sequence_type (tral.repeat.repeat.Repeat attribute)
set_circle_transition_probability_hmmer3() (tral.hmm.hmm.HMM method)
set_emission_probability_hmmer3() (tral.hmm.hmm.HMM method)
set_repeatlist() (tral.sequence.sequence.Sequence method)
set_transition_probability_hmmer3() (tral.hmm.hmm.HMM method)
shared_char() (in module tral.repeat_list.repeat_list)
shuffle_seq() (in module tral.search.search_hmm)
split_HMMER3_file() (in module tral.hmm.hmm_io)
split_sequence() (in module tral.sequence.repeat_detection_run)
states (tral.hmm.hmm.HMM attribute)
T
test() (in module tral.hmm.hmm_own_model)
text (tral.repeat.repeat.Repeat attribute)
TN93() (in module tral.repeat.repeat_score)
to_fixed_width() (in module tral.hmm.hmm_io)
to_line() (tral.search.search_hmm.TralHit method)
to_treks() (tral.search.search_hmm.TralHit method)
TR (class in tral.hmm.hmm_own_model)
tral.hmm.hmm
module
tral.hmm.hmm_io
module
tral.hmm.hmm_own_model
module
tral.hmm.hmm_viterbi
module
tral.repeat.repeat
module
tral.repeat.repeat_align
module
tral.repeat.repeat_exon
module
tral.repeat.repeat_io
module
tral.repeat.repeat_pvalue
module
tral.repeat.repeat_score
module
tral.repeat_list.repeat_list
module
tral.repeat_list.repeat_list_io
module
tral.search.filter_hmm
module
tral.search.search_hmm
module
tral.sequence.repeat_detection_io
module
tral.sequence.repeat_detection_run
module
tral.sequence.sequence
module
tral.sequence.sequence_io
module
TralHit (class in tral.search.search_hmm)
tred_get_repeats() (in module tral.sequence.repeat_detection_io)
tred_msa_from_pairwise() (in module tral.sequence.repeat_detection_io)
treks_get_repeats() (in module tral.sequence.repeat_detection_io)
trf_get_repeats() (in module tral.sequence.repeat_detection_io)
trust_fill_repeats() (in module tral.sequence.repeat_detection_io)
trust_get_repeats() (in module tral.sequence.repeat_detection_io)
two_repeats_overlap() (in module tral.repeat_list.repeat_list)
V
viterbi() (in module tral.hmm.hmm_viterbi)
viterbi_with_prob() (in module tral.hmm.hmm_viterbi)
W
write() (in module tral.sequence.sequence_io)
(tral.hmm.hmm.HMM method)
(tral.repeat.repeat.Repeat method)
(tral.repeat_list.repeat_list.RepeatList method)
(tral.sequence.sequence.Sequence method)
write_hits() (in module tral.search.filter_hmm)
write_HMMER() (in module tral.hmm.hmm_io)
write_treks() (in module tral.search.filter_hmm)
X
xstream_get_repeats() (in module tral.sequence.repeat_detection_io)