SIMD String Matching and Sequence Alignment

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Documentation for package ‘stridealign’ version 0.6.0

• DESCRIPTION file

Help Pages

A B C D E H I J K L M N O P R S T W

-- A --

AlignmentPath	Canonical sequence-alignment APIs
AlignmentResult	Canonical sequence-alignment APIs
ascii_matrix	Substitution matrices for sequence alignment
ascii_text	Substitution matrices for sequence alignment
available_backends	Canonical backend inspection API

-- B --

BackendKind	Canonical backend inspection API
BackendRecord	Canonical backend inspection API
backend_is_available	Canonical backend inspection API
beider_morse	Phonetic encoders and comparisons
blosum100	Substitution matrices for sequence alignment
blosum30	Substitution matrices for sequence alignment
blosum35	Substitution matrices for sequence alignment
blosum40	Substitution matrices for sequence alignment
blosum45	Substitution matrices for sequence alignment
blosum50	Substitution matrices for sequence alignment
blosum55	Substitution matrices for sequence alignment
blosum60	Substitution matrices for sequence alignment
blosum62	Substitution matrices for sequence alignment
blosum65	Substitution matrices for sequence alignment
blosum70	Substitution matrices for sequence alignment
blosum75	Substitution matrices for sequence alignment
blosum80	Substitution matrices for sequence alignment
blosum85	Substitution matrices for sequence alignment
blosum90	Substitution matrices for sequence alignment
BmpmRuleType	Phonetic encoders and comparisons

-- C --

caverphone	Phonetic encoders and comparisons
cdist	Python-style pair, batch, selection, and cdist APIs
cdist_above_threshold	Python-style pair, batch, selection, and cdist APIs
cdist_top_k	Python-style pair, batch, selection, and cdist APIs
cdist_top_k_per_query	Python-style pair, batch, selection, and cdist APIs
cologne_phonetic	Phonetic encoders and comparisons
cosine	Additional native string similarities
cosine_similarities	Additional native string similarities

-- D --

daitch_mokotoff	Phonetic encoders and comparisons
damerau_levenshtein_best	Python-style pair, batch, selection, and cdist APIs
damerau_levenshtein_normalized_best	Python-style pair, batch, selection, and cdist APIs
damerau_levenshtein_normalized_score	Python-style pair, batch, selection, and cdist APIs
damerau_levenshtein_normalized_scores	Python-style pair, batch, selection, and cdist APIs
damerau_levenshtein_normalized_top_k	Python-style pair, batch, selection, and cdist APIs
damerau_levenshtein_score	Python-style pair, batch, selection, and cdist APIs
damerau_levenshtein_scores	Python-style pair, batch, selection, and cdist APIs
damerau_levenshtein_top_k	Python-style pair, batch, selection, and cdist APIs
detect_best_backend	Canonical backend inspection API
dice	Additional native string similarities
dice_similarities	Additional native string similarities
dna_match	Substitution matrices for sequence alignment
DoubleMetaphoneVariant	Phonetic encoders and comparisons
double_metaphone	Phonetic encoders and comparisons
dtw	Dynamic Time Warping distances
dtw_distances	Dynamic Time Warping distances

-- E --

extract	Python-style pair, batch, selection, and cdist APIs
extract_best	Python-style pair, batch, selection, and cdist APIs

-- H --

hamming_best	Python-style pair, batch, selection, and cdist APIs
hamming_normalized_best	Python-style pair, batch, selection, and cdist APIs
hamming_normalized_score	Python-style pair, batch, selection, and cdist APIs
hamming_normalized_scores	Python-style pair, batch, selection, and cdist APIs
hamming_normalized_top_k	Python-style pair, batch, selection, and cdist APIs
hamming_score	Python-style pair, batch, selection, and cdist APIs
hamming_scores	Python-style pair, batch, selection, and cdist APIs
hamming_top_k	Python-style pair, batch, selection, and cdist APIs

-- I --

identity_matrix	Substitution matrices for sequence alignment
indel_best	Python-style pair, batch, selection, and cdist APIs
indel_normalized_best	Python-style pair, batch, selection, and cdist APIs
indel_normalized_score	Python-style pair, batch, selection, and cdist APIs
indel_normalized_scores	Python-style pair, batch, selection, and cdist APIs
indel_normalized_top_k	Python-style pair, batch, selection, and cdist APIs
indel_score	Python-style pair, batch, selection, and cdist APIs
indel_scores	Python-style pair, batch, selection, and cdist APIs
indel_top_k	Python-style pair, batch, selection, and cdist APIs

-- J --

jaccard	Additional native string similarities
jaccard_similarities	Additional native string similarities
jaro_best	Python-style pair, batch, selection, and cdist APIs
jaro_similarities	Python-style pair, batch, selection, and cdist APIs
jaro_similarity	Python-style pair, batch, selection, and cdist APIs
jaro_top_k	Python-style pair, batch, selection, and cdist APIs
jaro_winkler_best	Python-style pair, batch, selection, and cdist APIs
jaro_winkler_similarities	Python-style pair, batch, selection, and cdist APIs
jaro_winkler_similarity	Python-style pair, batch, selection, and cdist APIs
jaro_winkler_top_k	Python-style pair, batch, selection, and cdist APIs

-- K --

keyboard	Keyboard-aware substitution matrices
keyboard_available	Keyboard-aware substitution matrices
keyboard_from_confusion_counts	Keyboard-aware substitution matrices
keyboard_from_npy	Keyboard-aware substitution matrices

-- L --

lcs_length	Additional native string similarities
lcs_substring	Additional native string similarities
lcs_substring_length	Additional native string similarities
LevenshteinScorer	Python-style pair, batch, selection, and cdist APIs
levenshtein_best	Python-style pair, batch, selection, and cdist APIs
levenshtein_normalized_best	Python-style pair, batch, selection, and cdist APIs
levenshtein_normalized_score	Python-style pair, batch, selection, and cdist APIs
levenshtein_normalized_scores	Python-style pair, batch, selection, and cdist APIs
levenshtein_normalized_top_k	Python-style pair, batch, selection, and cdist APIs
levenshtein_score	Python-style pair, batch, selection, and cdist APIs
levenshtein_scores	Python-style pair, batch, selection, and cdist APIs
levenshtein_top_k	Python-style pair, batch, selection, and cdist APIs

-- M --

match_rating_codex	Phonetic encoders and comparisons
match_rating_compare	Phonetic encoders and comparisons
metaphone	Phonetic encoders and comparisons
MetaphoneVariant	Phonetic encoders and comparisons
metaphone_equal	Phonetic encoders and comparisons
monge_elkan	Additional native string similarities

-- N --

needleman_wunsch_cigar	Canonical sequence-alignment APIs
needleman_wunsch_normalized_score	Canonical sequence-alignment APIs
needleman_wunsch_normalized_scores	Canonical sequence-alignment APIs
needleman_wunsch_path	Canonical sequence-alignment APIs
needleman_wunsch_path_info	Canonical sequence-alignment APIs
needleman_wunsch_score	Canonical sequence-alignment APIs
needleman_wunsch_scores	Canonical sequence-alignment APIs
needleman_wunsch_trace_cigar	Canonical sequence-alignment APIs
needleman_wunsch_trade_cigar	Canonical sequence-alignment APIs
nuc44	Substitution matrices for sequence alignment
nysiis	Phonetic encoders and comparisons
nysiis_equal	Phonetic encoders and comparisons

-- O --

overlap	Additional native string similarities
overlap_similarities	Additional native string similarities

-- P --

pam10	Substitution matrices for sequence alignment
pam100	Substitution matrices for sequence alignment
pam110	Substitution matrices for sequence alignment
pam120	Substitution matrices for sequence alignment
pam130	Substitution matrices for sequence alignment
pam140	Substitution matrices for sequence alignment
pam150	Substitution matrices for sequence alignment
pam160	Substitution matrices for sequence alignment
pam170	Substitution matrices for sequence alignment
pam180	Substitution matrices for sequence alignment
pam190	Substitution matrices for sequence alignment
pam20	Substitution matrices for sequence alignment
pam200	Substitution matrices for sequence alignment
pam210	Substitution matrices for sequence alignment
pam220	Substitution matrices for sequence alignment
pam230	Substitution matrices for sequence alignment
pam240	Substitution matrices for sequence alignment
pam250	Substitution matrices for sequence alignment
pam260	Substitution matrices for sequence alignment
pam270	Substitution matrices for sequence alignment
pam280	Substitution matrices for sequence alignment
pam290	Substitution matrices for sequence alignment
pam30	Substitution matrices for sequence alignment
pam300	Substitution matrices for sequence alignment
pam310	Substitution matrices for sequence alignment
pam320	Substitution matrices for sequence alignment
pam330	Substitution matrices for sequence alignment
pam340	Substitution matrices for sequence alignment
pam350	Substitution matrices for sequence alignment
pam360	Substitution matrices for sequence alignment
pam370	Substitution matrices for sequence alignment
pam380	Substitution matrices for sequence alignment
pam390	Substitution matrices for sequence alignment
pam40	Substitution matrices for sequence alignment
pam400	Substitution matrices for sequence alignment
pam410	Substitution matrices for sequence alignment
pam420	Substitution matrices for sequence alignment
pam430	Substitution matrices for sequence alignment
pam440	Substitution matrices for sequence alignment
pam450	Substitution matrices for sequence alignment
pam460	Substitution matrices for sequence alignment
pam470	Substitution matrices for sequence alignment
pam480	Substitution matrices for sequence alignment
pam490	Substitution matrices for sequence alignment
pam50	Substitution matrices for sequence alignment
pam500	Substitution matrices for sequence alignment
pam60	Substitution matrices for sequence alignment
pam70	Substitution matrices for sequence alignment
pam80	Substitution matrices for sequence alignment
pam90	Substitution matrices for sequence alignment
partial_ratio	Additional native string similarities
partial_token_set_ratio	Additional native string similarities
partial_token_sort_ratio	Additional native string similarities

-- R --

ratcliff_obershelp_similarities	Additional native string similarities
ratcliff_obershelp_similarity	Additional native string similarities

-- S --

Scorer	Python-style pair, batch, selection, and cdist APIs
Scores	Canonical sequence-alignment APIs
smith_waterman_best	Canonical sequence-alignment APIs
smith_waterman_cigar	Canonical sequence-alignment APIs
smith_waterman_farrar_normalized_score	Canonical sequence-alignment APIs
smith_waterman_farrar_normalized_scores	Canonical sequence-alignment APIs
smith_waterman_farrar_score	Canonical sequence-alignment APIs
smith_waterman_farrar_scores	Canonical sequence-alignment APIs
smith_waterman_normalized_score	Canonical sequence-alignment APIs
smith_waterman_normalized_scores	Canonical sequence-alignment APIs
smith_waterman_path	Canonical sequence-alignment APIs
smith_waterman_path_info	Canonical sequence-alignment APIs
smith_waterman_score	Canonical sequence-alignment APIs
smith_waterman_scores	Canonical sequence-alignment APIs
smith_waterman_top_k	Canonical sequence-alignment APIs
smith_waterman_trace_cigar	Canonical sequence-alignment APIs
smith_waterman_trade_cigar	Canonical sequence-alignment APIs
soundex	Phonetic encoders and comparisons
soundex_equal	Phonetic encoders and comparisons
stride_available_backends	Inspect stride-align SIMD dispatch
stride_backend	Inspect stride-align SIMD dispatch
stride_hamming	String distance and similarity
stride_hamming_similarity	String distance and similarity
stride_indel	String distance and similarity
stride_indel_similarity	String distance and similarity
stride_jaro	String distance and similarity
stride_jaro_winkler	String distance and similarity
stride_levenshtein	String distance and similarity
stride_levenshtein_similarity	String distance and similarity
stride_needleman_wunsch	Sequence-alignment scores
stride_needleman_wunsch_affine	Sequence-alignment scores
stride_osa	String distance and similarity
stride_osa_similarity	String distance and similarity
stride_smith_waterman	Sequence-alignment scores
stride_smith_waterman_affine	Sequence-alignment scores
stride_true_damerau_levenshtein	String distance and similarity
stride_true_damerau_levenshtein_similarity	String distance and similarity
SubstitutionMatrix	Substitution matrices for sequence alignment
substitution_matrix_encode	Substitution matrices for sequence alignment
substitution_matrix_from_ncbi_text	Substitution matrices for sequence alignment
substitution_matrix_score	Substitution matrices for sequence alignment
substitution_matrix_score_step_limit	Substitution matrices for sequence alignment
substitution_matrix_transpose	Substitution matrices for sequence alignment

-- T --

token_set_ratio	Additional native string similarities
token_sort_ratio	Additional native string similarities
true_damerau_levenshtein_best	Python-style pair, batch, selection, and cdist APIs
true_damerau_levenshtein_normalized_best	Python-style pair, batch, selection, and cdist APIs
true_damerau_levenshtein_normalized_score	Python-style pair, batch, selection, and cdist APIs
true_damerau_levenshtein_normalized_scores	Python-style pair, batch, selection, and cdist APIs
true_damerau_levenshtein_normalized_top_k	Python-style pair, batch, selection, and cdist APIs
true_damerau_levenshtein_score	Python-style pair, batch, selection, and cdist APIs
true_damerau_levenshtein_scores	Python-style pair, batch, selection, and cdist APIs
true_damerau_levenshtein_top_k	Python-style pair, batch, selection, and cdist APIs

-- W --

WRatio

Additional native string similarities