├── .Rbuildignore ├── .github └── workflows │ └── test-coverage.yaml ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── AMINO_ACID_CODE.R ├── GENETIC_CODE.R ├── IUPAC_CODE_MAP.R ├── MIndex-class.R ├── MaskedXString-class.R ├── MultipleAlignment.R ├── PDict-class.R ├── QualityScaledXStringSet.R ├── SparseList-class.R ├── XString-class.R ├── XStringCodec-class.R ├── XStringQuality-class.R ├── XStringSet-class.R ├── XStringSet-comparison.R ├── XStringSet-io.R ├── XStringSetList-class.R ├── XStringViews-class.R ├── chartr.R ├── coloring.R ├── dinucleotideFrequencyTest.R ├── findPalindromes.R ├── getSeq.R ├── injectHardMask.R ├── lcsuffix.R ├── letter.R ├── letterFrequency.R ├── longestConsecutive.R ├── lowlevel-matching.R ├── maskMotif.R ├── match-utils.R ├── matchLRPatterns.R ├── matchPDict.R ├── matchPWM.R ├── matchPattern.R ├── matchProbePair.R ├── misc.R ├── padAndClip.R ├── predefined_scoring_matrices.R ├── replaceAt.R ├── replaceLetterAt.R ├── reverseComplement.R ├── seqinfo-methods.R ├── seqtype.R ├── strsplit-methods.R ├── toComplex.R ├── translate.R ├── trimLRPatterns.R ├── utils.R ├── xscat.R └── zzz.R ├── README.md ├── TODO ├── data ├── BLOSUM100.rda ├── BLOSUM45.rda ├── BLOSUM50.rda ├── BLOSUM62.rda ├── BLOSUM80.rda ├── HNF4alpha.rda ├── PAM120.rda ├── PAM250.rda ├── PAM30.rda ├── PAM40.rda ├── PAM70.rda └── yeastSEQCHR1.rda ├── inst ├── extdata │ ├── Phylip.txt │ ├── README │ ├── Sc.fa │ ├── Sp.fa │ ├── dm3_upstream2000.fa.gz │ ├── fastaEx.fa │ ├── hg18chr8_gap.txt │ ├── hg18chrY_gap.txt │ ├── msx2_mRNA.aln │ ├── s_1_sequence.txt │ ├── someORF.fa │ └── someORF.fa.gz ├── include │ ├── Biostrings_defines.h │ ├── Biostrings_interface.h │ └── _Biostrings_stubs.c └── unitTests │ ├── test_MultipleAlignment.R │ ├── test_XString.R │ ├── test_matchDNAPattern.R.FIXME │ ├── test_seqinfo-methods.R │ └── test_twoWayAlphabetFrequency.R ├── legacy ├── CHANGES_Biostrings_2_vs_Biostrings_1 └── rgrep-tip.txt ├── man ├── AAString-class.Rd ├── AMINO_ACID_CODE.Rd ├── Biostrings-internals.Rd ├── DNAString-class.Rd ├── GENETIC_CODE.Rd ├── HNF4alpha.Rd ├── IUPAC_CODE_MAP.Rd ├── MIndex-class.Rd ├── MaskedXString-class.Rd ├── MultipleAlignment-class.Rd ├── PDict-class.Rd ├── QualityScaledXStringSet-class.Rd ├── RNAString-class.Rd ├── XString-class.Rd ├── XStringQuality-class.Rd ├── XStringSet-class.Rd ├── XStringSet-comparison.Rd ├── XStringSet-io.Rd ├── XStringSetList-class.Rd ├── XStringViews-class.Rd ├── chartr.Rd ├── coloring.Rd ├── detail.Rd ├── dinucleotideFrequencyTest.Rd ├── findPalindromes.Rd ├── getSeq.Rd ├── gregexpr2.Rd ├── injectHardMask.Rd ├── lcsuffix.Rd ├── letter.Rd ├── letterFrequency.Rd ├── longestConsecutive.Rd ├── lowlevel-matching.Rd ├── maskMotif.Rd ├── match-utils.Rd ├── matchLRPatterns.Rd ├── matchPDict-exact.Rd ├── matchPDict-inexact.Rd ├── matchPWM.Rd ├── matchPattern.Rd ├── matchProbePair.Rd ├── misc.Rd ├── nucleotideFrequency.Rd ├── padAndClip.Rd ├── predefined_scoring_matrices.Rd ├── replaceAt.Rd ├── replaceLetterAt.Rd ├── reverseComplement.Rd ├── seqinfo-methods.Rd ├── toComplex.Rd ├── translate.Rd ├── trimLRPatterns.Rd ├── xscat.Rd └── yeastSEQCHR1.Rd ├── src ├── BAB_class.c ├── Biostrings.h ├── BitMatrix.c ├── IRanges_stubs.c ├── MIndex_class.c ├── PreprocessedTB_class.c ├── R_init_Biostrings.c ├── RoSeqs_utils.c ├── S4Vectors_stubs.c ├── SparseList_utils.c ├── XStringSetList_class.c ├── XStringSet_class.c ├── XString_class.c ├── XVector_stubs.c ├── find_palindromes.c ├── gtestsim.c ├── inject_code.c ├── lcsuffix.c ├── letter_frequency.c ├── lowlevel_matching.c ├── match_PWM.c ├── match_pattern.c ├── match_pattern_boyermoore.c ├── match_pattern_indels.c ├── match_pattern_shiftor.c ├── match_pdict.c ├── match_pdict_ACtree2.c ├── match_pdict_Twobit.c ├── match_pdict_utils.c ├── match_reporting.c ├── read_fasta_files.c ├── read_fastq_files.c ├── replaceAt.c ├── replace_letter_at.c ├── strutils.c ├── translate.c ├── unstrsplit_methods.c ├── utils.c └── xscat.c ├── tests ├── testthat.R └── testthat │ ├── helpers.R │ ├── test-MaskedXString.R │ ├── test-MultipleAlignment-class.R │ ├── test-OtherMasking.R │ ├── test-PDict.R │ ├── test-QualityScaledXStringSet.R │ ├── test-XString-class.R │ ├── test-XStringQuality.R │ ├── test-XStringSet-class.R │ ├── test-XStringSet-comparison.R │ ├── test-XStringSet-io.R │ ├── test-XStringSetList-class.R │ ├── test-XStringSetList.R │ ├── test-XStringViews.R │ ├── test-chartr.R │ ├── test-coloring.R │ ├── test-dinucleotideFrequencyTest.R │ ├── test-findPalindromes.R │ ├── test-letter.R │ ├── test-letterFrequency.R │ ├── test-longestConsecutive.R │ ├── test-matchLRPatterns.R │ ├── test-matchPDict.R │ ├── test-matchPWM.R │ ├── test-matchPattern.R │ ├── test-misc.R │ ├── test-padAndClip.R │ ├── test-replaceAt.R │ ├── test-strsplit-methods.R │ ├── test-toComplex.R │ ├── test-translate.R │ ├── test-trimLRPatterns.R │ ├── test-utils.R │ └── test-xscat.R └── vignettes ├── Biostrings2Classes.Rnw ├── BiostringsQuickOverview.Rnw ├── 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