Index

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)