├── .Rbuildignore ├── .github ├── .gitignore ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md └── workflows │ ├── check-bioc.yml │ └── rhub.yaml ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── RcppExports.R ├── alphabet.R ├── bite.R ├── catch-routine-registration.R ├── collapse.R ├── complement.R ├── doc-sq-class.R ├── doc-tidysq.R ├── export_sq.R ├── find_invalid_letters.R ├── find_motifs.R ├── has.R ├── import_sq.R ├── is_empty_sq.R ├── paste.R ├── random_sq.R ├── read_fasta.R ├── remove_ambiguous.R ├── remove_na.R ├── reverse.R ├── sq.R ├── sqapply.R ├── substitute_letters.R ├── sysdata.rda ├── translate.R ├── typify.R ├── util-checkmate-functions.R ├── util-conditions.R ├── util-format.R ├── util-methods.R ├── util-options.R ├── util-pack.R ├── util-print.R ├── util-type.R ├── util-unpack.R ├── util-vctrs-cast.R ├── util-vctrs-names.R ├── util-vctrs-prototypes.R ├── write_fasta.R └── zzz.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── codecov.yml ├── cran-comments.md ├── docs ├── 404.html ├── apple-touch-icon-120x120.png ├── apple-touch-icon-152x152.png ├── apple-touch-icon-180x180.png ├── apple-touch-icon-60x60.png ├── apple-touch-icon-76x76.png ├── apple-touch-icon.png ├── articles │ ├── advanced-alphabet.html │ ├── advanced-alphabet_files │ │ └── header-attrs-2.9 │ │ │ └── header-attrs.js │ ├── index.html │ ├── quick-start.html │ └── quick-start_files │ │ └── header-attrs-2.9 │ │ └── header-attrs.js ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── favicon-16x16.png ├── favicon-32x32.png ├── favicon.ico ├── index.html ├── link.svg ├── logo.png ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml └── reference │ ├── AAindex.html │ ├── BLOSUM50.html │ ├── BLOSUM50_enc.html │ ├── BLOSUM50_pca.html │ ├── BLOSUM62.html │ ├── BLOSUM62_enc.html │ ├── BLOSUM62_pca.html │ ├── Rplot001.png │ ├── alphabet.html │ ├── aminoacids_df.html │ ├── as.character.sq.html │ ├── as.matrix.sq.html │ ├── as.sq.html │ ├── bg_freqs.html │ ├── bite.html │ ├── c.sq.html │ ├── clean.html │ ├── collapse.html │ ├── complement.html │ ├── construct_sq.html │ ├── count_kmers.html │ ├── encode.html │ ├── encsq_to_list.html │ ├── equals-.sq.html │ ├── export_sq.html │ ├── extract_kmers.html │ ├── fast-mode.html │ ├── figures │ ├── lifecycle-archived.svg │ ├── lifecycle-defunct.svg │ ├── lifecycle-deprecated.svg │ ├── lifecycle-experimental.svg │ ├── lifecycle-maturing.svg │ ├── lifecycle-questioning.svg │ ├── lifecycle-soft-deprecated.svg │ ├── lifecycle-stable.svg │ ├── lifecycle-superseded.svg │ └── logo.png │ ├── find_invalid_letters.html │ ├── find_motifs.html │ ├── get_invalid_letters.html │ ├── get_sq_alphabet.html │ ├── get_sq_lengths.html │ ├── get_sq_type.html │ ├── get_standard_alphabet.html │ ├── get_tidysq_options.html │ ├── grapes-has-grapes.html │ ├── import_sq.html │ ├── index.html │ ├── is.sq.html │ ├── is_empty_sq.html │ ├── is_null_sq.html │ ├── nucleotides_df.html │ ├── paste.html │ ├── print.sq.html │ ├── random_sq.html │ ├── read_fasta.html │ ├── remove_ambiguous.html │ ├── remove_na.html │ ├── reverse.html │ ├── sq-class.html │ ├── sq.html │ ├── sq_type.html │ ├── sqapply.html │ ├── sqconcatenate.html │ ├── sqextract.html │ ├── sqprint.html │ ├── substitute_letters.html │ ├── tidysq-options.html │ ├── tidysq-package.html │ ├── translate.html │ ├── typify.html │ └── write_fasta.html ├── inst ├── WORDLIST ├── examples │ └── example_aa.fasta └── include │ ├── tidysq.h │ └── tidysq │ ├── Alphabet.h │ ├── ProtoSequence.h │ ├── ProtoSequenceInputInterpreter.h │ ├── ProtoSq.h │ ├── Proxy.h │ ├── Rcpp-export.h │ ├── Rcpp-import.h │ ├── Sequence.h │ ├── Sq.h │ ├── collapse.h │ ├── constants │ ├── WarningLevel.h │ ├── ambiguous_maps.h │ ├── complement_tables.h │ ├── io.h │ ├── standard_letters.h │ └── translate_tables.h │ ├── find_motifs.h │ ├── internal │ ├── LetterTree.h │ ├── Motif.h │ ├── MotifFrame.h │ ├── obtain_alphabet.h │ ├── pack.h │ ├── unpack_common.h │ └── unpack_multichar.h │ ├── io │ ├── read_fasta.h │ └── write_fasta.h │ ├── ops │ ├── Operation.h │ ├── apply_R_function.h │ ├── bite.h │ ├── complement.h │ ├── find_invalid_letters.h │ ├── has.h │ ├── pack.h │ ├── random_sq.h │ ├── remove_NA.h │ ├── remove_ambiguous.h │ ├── remove_on_condition.h │ ├── reverse.h │ ├── skip.h │ ├── substitute_letters.h │ ├── translate.h │ ├── typify.h │ └── unpack.h │ ├── paste.h │ ├── sq-types.h │ ├── sqapply.h │ ├── tidysq-typedefs.h │ └── util │ ├── ResultWrapper.h │ ├── calculate_length.h │ ├── find_common_size.h │ ├── handle_warning_message.h │ ├── match_letter.h │ ├── obtain_alphabet.h │ ├── random.h │ └── transform-common.h ├── man ├── alphabet.Rd ├── as.character.sq.Rd ├── as.matrix.sq.Rd ├── as.sq.Rd ├── bite.Rd ├── collapse.Rd ├── complement.Rd ├── equals-.sq.Rd ├── export_sq.Rd ├── figures │ ├── lifecycle-archived.svg │ ├── lifecycle-defunct.svg │ ├── lifecycle-deprecated.svg │ ├── lifecycle-experimental.svg │ ├── lifecycle-maturing.svg │ ├── lifecycle-questioning.svg │ ├── lifecycle-soft-deprecated.svg │ ├── lifecycle-stable.svg │ ├── lifecycle-superseded.svg │ └── logo.png ├── find_invalid_letters.Rd ├── find_motifs.Rd ├── get_sq_lengths.Rd ├── get_standard_alphabet.Rd ├── get_tidysq_options.Rd ├── grapes-has-grapes.Rd ├── import_sq.Rd ├── is.sq.Rd ├── is_empty_sq.Rd ├── paste.Rd ├── random_sq.Rd ├── read_fasta.Rd ├── remove_ambiguous.Rd ├── remove_na.Rd ├── reverse.Rd ├── roxygen │ ├── meta.R │ └── templates │ │ ├── NA_letter.R │ │ ├── alphabet.R │ │ ├── by_letter.R │ │ ├── dest_type.R │ │ ├── dot-name.R │ │ ├── dot-sq.R │ │ ├── ignore_case.R │ │ ├── motif_details.R │ │ ├── name.R │ │ ├── on_warning.R │ │ ├── safe_mode.R │ │ ├── three-dots.R │ │ └── x.R ├── sq-class.Rd ├── sq.Rd ├── sq_type.Rd ├── sqapply.Rd ├── sqconcatenate.Rd ├── sqextract.Rd ├── sqprint.Rd ├── substitute_letters.Rd ├── tidysq-package.Rd ├── translate.Rd ├── typify.Rd └── write_fasta.Rd ├── pkgdown └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── renv.lock ├── renv ├── .gitignore ├── activate.R └── settings.dcf ├── src ├── Makevars ├── Makevars.win ├── RcppExports.cpp ├── apply_R_function.cpp ├── bite.cpp ├── collapse.cpp ├── complement.cpp ├── find_invalid_letters.cpp ├── find_motifs.cpp ├── get_standard_alphabet.cpp ├── guess_standard_alph.cpp ├── has.cpp ├── obtain_alphabet.cpp ├── pack.cpp ├── paste.cpp ├── random_sq.cpp ├── read_fasta.cpp ├── remove_NA.cpp ├── remove_ambiguous.cpp ├── reverse.cpp ├── sqapply.cpp ├── substitute_letters.cpp ├── test-pack.cpp ├── test-runner.cpp ├── translate.cpp ├── typify.cpp ├── unpack.cpp └── write_fasta.cpp ├── tests ├── spelling.R ├── testthat.R └── testthat │ ├── setup-tests.R │ ├── test-alphabet.R │ 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