!=,BString,character-method	XString-class
!=,character,BString-method	XString-class
!=,character,XStringViews-method	XStringViews-class
!=,XString,XString-method	XString-class
!=,XString,XStringViews-method	XStringViews-class
!=,XStringViews,character-method	XStringViews-class
!=,XStringViews,XString-method	XStringViews-class
!=,XStringViews,XStringViews-method	XStringViews-class
.inplaceReplaceLetterAt	replaceLetterAt
==,BString,character-method	XString-class
==,character,BString-method	XString-class
==,character,XStringViews-method	XStringViews-class
==,XString,XString-method	XString-class
==,XString,XStringViews-method	XStringViews-class
==,XStringViews,character-method	XStringViews-class
==,XStringViews,XString-method	XStringViews-class
==,XStringViews,XStringViews-method	XStringViews-class
AAString	AAString-class
AAString-class	AAString-class
AAStringSet	XStringSet-class
AAStringSet-class	XStringSet-class
AA_ALPHABET	AAString-class
ACtree	PDict-class
ACtree-class	PDict-class
ACtree2	PDict-class
ACtree2-class	PDict-class
adjacentViews	XStringViews-constructors
align-utils	align-utils
aligned	AlignedXStringSet-class
aligned,AlignedXStringSet-method	AlignedXStringSet-class
aligned,PairwiseAlignedFixedSubject-method	PairwiseAlignedFixedSubject-class
AlignedXStringSet	AlignedXStringSet-class
AlignedXStringSet-class	AlignedXStringSet-class
alignScore	needwunsQS
alignScore.needwunsQS	needwunsQS
alphabet	XString-class
alphabet,AAString-method	AAString-class
alphabet,AlignedXStringSet-method	AlignedXStringSet-class
alphabet,BString-method	XString-class
alphabet,DNAString-method	DNAString-class
alphabet,MaskedXString-method	MaskedXString-class
alphabet,PairwiseAlignedFixedSubject-method	PairwiseAlignedFixedSubject-class
alphabet,RNAString-method	RNAString-class
alphabet,XStringCodec-method	Biostrings-internals
alphabet,XStringSet-method	XStringSet-class
alphabet,XStringViews-method	XStringViews-class
alphabetFrequency	alphabetFrequency
alphabetFrequency,DNAString-method	alphabetFrequency
alphabetFrequency,DNAStringSet-method	alphabetFrequency
alphabetFrequency,MaskedXString-method	alphabetFrequency
alphabetFrequency,RNAString-method	alphabetFrequency
alphabetFrequency,RNAStringSet-method	alphabetFrequency
alphabetFrequency,XString-method	alphabetFrequency
alphabetFrequency,XStringSet-method	alphabetFrequency
alphabetFrequency,XStringViews-method	alphabetFrequency
AMINO_ACID_CODE	AMINO_ACID_CODE
append,QualityScaledXStringSet,QualityScaledXStringSet-method	QualityScaledXStringSet-class
append,XStringSet,XStringSet-method	XStringSet-class
as.character,AlignedXStringSet-method	AlignedXStringSet-class
as.character,MaskedXString-method	MaskedXString-class
as.character,PairwiseAlignedFixedSubject-method	PairwiseAlignedFixedSubject-class
as.character,XString-method	XString-class
as.character,XStringSet-method	XStringSet-class
as.character,XStringViews-method	XStringViews-class
as.complex,DNAString-method	toComplex
as.integer,PhredQuality-method	XStringQuality-class
as.integer,SolexaQuality-method	XStringQuality-class
as.list,MTB_PDict-method	PDict-class
as.list,SparseList-method	Biostrings-internals
as.matrix,ACtree-method	PDict-class
as.matrix,PairwiseAlignedFixedSubject-method	PairwiseAlignedFixedSubject-class
as.matrix,XStringSet-method	XStringSet-class
as.matrix,XStringViews-method	XStringViews-class
as.numeric,PhredQuality-method	XStringQuality-class
as.numeric,SolexaQuality-method	XStringQuality-class
BLOSUM100	substitution_matrices
BLOSUM45	substitution_matrices
BLOSUM50	substitution_matrices
BLOSUM62	substitution_matrices
BLOSUM80	substitution_matrices
BOC2_SubjectString	BOC_SubjectString-class
BOC2_SubjectString-class	BOC_SubjectString-class
BOC_SubjectString	BOC_SubjectString-class
BOC_SubjectString-class	BOC_SubjectString-class
BString	XString-class
BString-class	XString-class
BStringSet	XStringSet-class
BStringSet-class	XStringSet-class
BStringViews	XStringViews-constructors
BStringViews,ANY-method	XStringViews-constructors
BStringViews,file-method	XStringViews-constructors
BStringViews,XString-method	XStringViews-constructors
BStringViews,XStringViews-method	XStringViews-constructors
ByPos_MIndex-class	MIndex-class
cDNA	translate
CharacterToFASTArecords	XStringSet-io
chartr	chartr
chartr,MaskedXString-method	chartr
chartr,XString-method	chartr
chartr,XStringSet-method	chartr
chartr,XStringViews-method	chartr
class:AAString	AAString-class
class:AAStringSet	XStringSet-class
class:ACtree	PDict-class
class:ACtree2	PDict-class
class:AlignedXStringSet	AlignedXStringSet-class
class:BOC2_SubjectString	BOC_SubjectString-class
class:BOC_SubjectString	BOC_SubjectString-class
class:BString	XString-class
class:BStringSet	XStringSet-class
class:ByPos_MIndex	MIndex-class
class:DNAString	DNAString-class
class:DNAStringSet	XStringSet-class
class:Dups	Biostrings-internals
class:InDel	InDel-class
class:MaskedAAString	MaskedXString-class
class:MaskedBString	MaskedXString-class
class:MaskedDNAString	MaskedXString-class
class:MaskedRNAString	MaskedXString-class
class:MaskedXString	MaskedXString-class
class:MIndex	MIndex-class
class:MTB_PDict	PDict-class
class:PairwiseAlignedFixedSubject	PairwiseAlignedFixedSubject-class
class:PairwiseAlignedFixedSubjectSummary	PairwiseAlignedFixedSubject-class
class:PDict	PDict-class
class:PDict3Parts	PDict-class
class:PhredQuality	XStringQuality-class
class:PreprocessedTB	PDict-class
class:QualityAlignedXStringSet	AlignedXStringSet-class
class:QualityScaledAAStringSet	QualityScaledXStringSet-class
class:QualityScaledBStringSet	QualityScaledXStringSet-class
class:QualityScaledDNAStringSet	QualityScaledXStringSet-class
class:QualityScaledRNAStringSet	QualityScaledXStringSet-class
class:QualityScaledXStringSet	QualityScaledXStringSet-class
class:RNAString	RNAString-class
class:RNAStringSet	XStringSet-class
class:SolexaQuality	XStringQuality-class
class:SparseList	Biostrings-internals
class:TB_PDict	PDict-class
class:Twobit	PDict-class
class:XString	XString-class
class:XStringCodec	Biostrings-internals
class:XStringPartialMatches	XStringPartialMatches-class
class:XStringQuality	XStringQuality-class
class:XStringSet	XStringSet-class
class:XStringViews	XStringViews-class
codons	translate
codons,DNAString-method	translate
codons,MaskedDNAString-method	translate
codons,MaskedRNAString-method	translate
codons,RNAString-method	translate
coerce,AAString,MaskedAAString-method	MaskedXString-class
coerce,BString,MaskedBString-method	MaskedXString-class
coerce,BString,PhredQuality-method	XStringQuality-class
coerce,BString,SolexaQuality-method	XStringQuality-class
coerce,BStringSet,PhredQuality-method	XStringQuality-class
coerce,BStringSet,SolexaQuality-method	XStringQuality-class
coerce,character,PhredQuality-method	XStringQuality-class
coerce,character,SolexaQuality-method	XStringQuality-class
coerce,DNAString,MaskedDNAString-method	MaskedXString-class
coerce,integer,PhredQuality-method	XStringQuality-class
coerce,integer,SolexaQuality-method	XStringQuality-class
coerce,MaskedAAString,AAString-method	MaskedXString-class
coerce,MaskedBString,BString-method	MaskedXString-class
coerce,MaskedDNAString,DNAString-method	MaskedXString-class
coerce,MaskedRNAString,RNAString-method	MaskedXString-class
coerce,MaskedXString,MaskCollection-method	MaskedXString-class
coerce,MaskedXString,NormalIRanges-method	MaskedXString-class
coerce,MaskedXString,XStringViews-method	MaskedXString-class
coerce,numeric,PhredQuality-method	XStringQuality-class
coerce,numeric,SolexaQuality-method	XStringQuality-class
coerce,PhredQuality,integer-method	XStringQuality-class
coerce,PhredQuality,numeric-method	XStringQuality-class
coerce,RNAString,MaskedRNAString-method	MaskedXString-class
coerce,SolexaQuality,integer-method	XStringQuality-class
coerce,SolexaQuality,numeric-method	XStringQuality-class
coerce,XStringSet,AAStringSet-method	XStringSet-class
coerce,XStringSet,BStringSet-method	XStringSet-class
coerce,XStringSet,DNAStringSet-method	XStringSet-class
coerce,XStringSet,RNAStringSet-method	XStringSet-class
compareStrings	align-utils
compareStrings,AlignedXStringSet,AlignedXStringSet-method	align-utils
compareStrings,character,character-method	align-utils
compareStrings,PairwiseAlignedFixedSubject,missing-method	align-utils
compareStrings,XString,XString-method	align-utils
compareStrings,XStringSet,XStringSet-method	align-utils
complement	reverse
complement,DNAString-method	reverse
complement,DNAStringSet-method	reverse
complement,MaskedDNAString-method	reverse
complement,MaskedRNAString-method	reverse
complement,RNAString-method	reverse
complement,RNAStringSet-method	reverse
complement,XStringViews-method	reverse
complementedPalindromeArmLength	findPalindromes
complementedPalindromeArmLength,DNAString-method	findPalindromes
complementedPalindromeArmLength,XStringViews-method	findPalindromes
complementedPalindromeLeftArm	findPalindromes
complementedPalindromeLeftArm,DNAString-method	findPalindromes
complementedPalindromeLeftArm,XStringViews-method	findPalindromes
complementedPalindromeRightArm	findPalindromes
complementedPalindromeRightArm,DNAString-method	findPalindromes
complementedPalindromeRightArm,XStringViews-method	findPalindromes
consensusMatrix	align-utils
consensusMatrix,character-method	align-utils
consensusMatrix,list-method	align-utils
consensusMatrix,matrix-method	align-utils
consensusMatrix,PairwiseAlignedFixedSubject-method	align-utils
consensusMatrix,XStringSet-method	align-utils
consensusMatrix,XStringViews-method	align-utils
consensusString	align-utils
consensusString,ANY-method	align-utils
consmat	align-utils
consmat,ANY-method	align-utils
countIndex	MIndex-class
countIndex,ByPos_MIndex-method	MIndex-class
countIndex,MIndex-method	MIndex-class
countPattern	matchPattern
countPattern,BOC2_SubjectString-method	BOC_SubjectString-class
countPattern,character-method	matchPattern
countPattern,MaskedXString-method	matchPattern
countPattern,XString-method	matchPattern
countPattern,XStringSet-method	matchPattern
countPattern,XStringViews-method	matchPattern
countPDict	matchPDict-exact
countPDict,MaskedXString-method	matchPDict-exact
countPDict,XString-method	matchPDict-exact
countPDict,XStringSet-method	matchPDict-exact
countPDict,XStringViews-method	matchPDict-exact
countPWM	matchPWM
coverage,AlignedXStringSet-method	align-utils
coverage,MaskedXString-method	match-utils
coverage,MIndex-method	match-utils
coverage,PairwiseAlignedFixedSubject-method	align-utils
coverage,PairwiseAlignedFixedSubjectSummary-method	align-utils
coverage,XStringViews-method	match-utils
deletion	InDel-class
deletion,InDel-method	InDel-class
dinucleotideFrequency	alphabetFrequency
dna2rna	translate
DNAString	DNAString-class
DNAString-class	DNAString-class
DNAStringSet	XStringSet-class
DNAStringSet-class	XStringSet-class
DNA_ALPHABET	DNAString-class
DNA_BASES	DNAString-class
duplicated,Dups-method	Biostrings-internals
duplicated,PDict-method	PDict-class
duplicated,PreprocessedTB-method	PDict-class
Dups	Biostrings-internals
Dups-class	Biostrings-internals
end,AlignedXStringSet-method	AlignedXStringSet-class
endIndex	MIndex-class
endIndex,ByPos_MIndex-method	MIndex-class
errorSubstitutionMatrices	substitution_matrices
extractAllMatches	matchPDict-exact
fasta.info	readFASTA
FASTArecordsToBStringViews	XStringSet-io
FASTArecordsToCharacter	XStringSet-io
FASTArecordsToXStringViews	XStringSet-io
findComplementedPalindromes	findPalindromes
findComplementedPalindromes,DNAString-method	findPalindromes
findComplementedPalindromes,MaskedXString-method	findPalindromes
findComplementedPalindromes,XStringViews-method	findPalindromes
findPalindromes	findPalindromes
findPalindromes,MaskedXString-method	findPalindromes
findPalindromes,XString-method	findPalindromes
findPalindromes,XStringViews-method	findPalindromes
gaps,MaskedXString-method	MaskedXString-class
GENETIC_CODE	GENETIC_CODE
gregexpr2	gregexpr2
hasOnlyBaseLetters	alphabetFrequency
hasOnlyBaseLetters,DNAString-method	alphabetFrequency
hasOnlyBaseLetters,DNAStringSet-method	alphabetFrequency
hasOnlyBaseLetters,MaskedDNAString-method	alphabetFrequency
hasOnlyBaseLetters,MaskedRNAString-method	alphabetFrequency
hasOnlyBaseLetters,RNAString-method	alphabetFrequency
hasOnlyBaseLetters,RNAStringSet-method	alphabetFrequency
hasOnlyBaseLetters,XStringViews-method	alphabetFrequency
head,PDict3Parts-method	PDict-class
head,TB_PDict-method	PDict-class
InDel	InDel-class
indel	AlignedXStringSet-class
indel,AlignedXStringSet-method	AlignedXStringSet-class
InDel-class	InDel-class
initialize,ACtree-method	PDict-class
initialize,ACtree2-method	PDict-class
initialize,AlignedXStringSet-method	AlignedXStringSet-class
initialize,BOC2_SubjectString-method	BOC_SubjectString-class
initialize,BOC_SubjectString-method	BOC_SubjectString-class
initialize,PairwiseAlignedFixedSubject-method	PairwiseAlignedFixedSubject-class
initialize,PreprocessedTB-method	PDict-class
initialize,QualityAlignedXStringSet-method	AlignedXStringSet-class
initialize,Twobit-method	PDict-class
initialize,XStringCodec-method	Biostrings-internals
injectHardMask	injectHardMask
injectHardMask,MaskedXString-method	injectHardMask
injectHardMask,XStringViews-method	injectHardMask
insertion	InDel-class
insertion,InDel-method	InDel-class
isMatching	match-utils
isMatchingAt	match-utils
isMatchingEndingAt	match-utils
isMatchingEndingAt,character-method	match-utils
isMatchingEndingAt,XString-method	match-utils
isMatchingStartingAt	match-utils
isMatchingStartingAt,character-method	match-utils
isMatchingStartingAt,XString-method	match-utils
IUPAC_CODE_MAP	IUPAC_CODE_MAP
lcprefix	pmatchPattern
lcprefix,character,character-method	pmatchPattern
lcprefix,character,XString-method	pmatchPattern
lcprefix,XString,character-method	pmatchPattern
lcprefix,XString,XString-method	pmatchPattern
lcsubstr	pmatchPattern
lcsubstr,character,character-method	pmatchPattern
lcsubstr,character,XString-method	pmatchPattern
lcsubstr,XString,character-method	pmatchPattern
lcsubstr,XString,XString-method	pmatchPattern
lcsuffix	pmatchPattern
lcsuffix,character,character-method	pmatchPattern
lcsuffix,character,XString-method	pmatchPattern
lcsuffix,XString,character-method	pmatchPattern
lcsuffix,XString,XString-method	pmatchPattern
length,AlignedXStringSet-method	AlignedXStringSet-class
length,Dups-method	Biostrings-internals
length,MaskedXString-method	MaskedXString-class
length,MIndex-method	MIndex-class
length,PairwiseAlignedFixedSubject-method	PairwiseAlignedFixedSubject-class
length,PairwiseAlignedFixedSubjectSummary-method	PairwiseAlignedFixedSubject-class
length,PDict-method	PDict-class
length,PDict3Parts-method	PDict-class
length,PreprocessedTB-method	PDict-class
length,SparseList-method	Biostrings-internals
length,XString-method	XString-class
length,XStringSet-method	XStringSet-class
letter	letter
letter,character-method	letter
letter,MaskedXString-method	letter
letter,XString-method	letter
letter,XStringViews-method	letter
ls,SparseList-method	Biostrings-internals
mask	maskMotif
MaskedAAString	MaskedXString-class
MaskedAAString-class	MaskedXString-class
MaskedBString	MaskedXString-class
MaskedBString-class	MaskedXString-class
MaskedDNAString	MaskedXString-class
MaskedDNAString-class	MaskedXString-class
maskedratio,MaskedXString-method	MaskedXString-class
MaskedRNAString	MaskedXString-class
MaskedRNAString-class	MaskedXString-class
maskedwidth,MaskedXString-method	MaskedXString-class
MaskedXString	MaskedXString-class
MaskedXString-class	MaskedXString-class
maskMotif	maskMotif
maskMotif,MaskedXString,character-method	maskMotif
maskMotif,MaskedXString,XString-method	maskMotif
maskMotif,XString,ANY-method	maskMotif
masks	MaskedXString-class
masks,MaskedXString-method	MaskedXString-class
masks,XString-method	MaskedXString-class
masks<-	MaskedXString-class
masks<-,MaskedXString,MaskCollection-method	MaskedXString-class
masks<-,MaskedXString,NULL-method	MaskedXString-class
masks<-,XString,ANY-method	MaskedXString-class
masks<-,XString,NULL-method	MaskedXString-class
match-utils	match-utils
matchDNAPattern	matchPattern
matchLRPatterns	matchLRPatterns
matchLRPatterns,MaskedXString-method	matchLRPatterns
matchLRPatterns,XString-method	matchLRPatterns
matchLRPatterns,XStringViews-method	matchLRPatterns
matchPattern	matchPattern
matchPattern,BOC2_SubjectString-method	BOC_SubjectString-class
matchPattern,BOC_SubjectString-method	BOC_SubjectString-class
matchPattern,character-method	matchPattern
matchPattern,MaskedXString-method	matchPattern
matchPattern,XString-method	matchPattern
matchPattern,XStringSet-method	matchPattern
matchPattern,XStringViews-method	matchPattern
matchPDict	matchPDict-exact
matchPDict,MaskedXString-method	matchPDict-exact
matchPDict,XString-method	matchPDict-exact
matchPDict,XStringSet-method	matchPDict-exact
matchPDict,XStringViews-method	matchPDict-exact
matchPDict-exact	matchPDict-exact
matchPDict-inexact	matchPDict-inexact
matchProbePair	matchProbePair
matchProbePair,DNAString-method	matchProbePair
matchProbePair,MaskedDNAString-method	matchProbePair
matchProbePair,XStringViews-method	matchProbePair
matchPWM	matchPWM
maxScore	matchPWM
maxWeights	matchPWM
mergeIUPACLetters	IUPAC_CODE_MAP
MIndex	MIndex-class
MIndex-class	MIndex-class
mismatch	match-utils
mismatch,AlignedXStringSet,missing-method	align-utils
mismatch,ANY,XStringViews-method	match-utils
mismatchSummary	align-utils
mismatchSummary,AlignedXStringSet-method	align-utils
mismatchSummary,PairwiseAlignedFixedSubject-method	align-utils
mismatchSummary,PairwiseAlignedFixedSubjectSummary-method	align-utils
mismatchSummary,QualityAlignedXStringSet-method	align-utils
mismatchTable	align-utils
mismatchTable,AlignedXStringSet-method	align-utils
mismatchTable,PairwiseAlignedFixedSubject-method	align-utils
mismatchTable,QualityAlignedXStringSet-method	align-utils
mkAllStrings	alphabetFrequency
MTB_PDict	PDict-class
MTB_PDict-class	PDict-class
names,MIndex-method	MIndex-class
names,PDict-method	PDict-class
names,XStringSet-method	XStringSet-class
names<-,MIndex-method	MIndex-class
names<-,PDict-method	PDict-class
names<-,XStringSet-method	XStringSet-class
narrow,QualityScaledXStringSet-method	QualityScaledXStringSet-class
narrow,XStringSet-method	XStringSet-class
nchar,AlignedXStringSet-method	AlignedXStringSet-class
nchar,MaskedXString-method	MaskedXString-class
nchar,PairwiseAlignedFixedSubject-method	PairwiseAlignedFixedSubject-class
nchar,PairwiseAlignedFixedSubjectSummary-method	PairwiseAlignedFixedSubject-class
nchar,XString-method	XString-class
nchar,XStringSet-method	XStringSet-class
nchar,XStringViews-method	XStringViews-class
neditAt	match-utils
neditEndingAt	match-utils
neditEndingAt,character-method	match-utils
neditEndingAt,XString-method	match-utils
neditStartingAt	match-utils
neditStartingAt,character-method	match-utils
neditStartingAt,XString-method	match-utils
needwunsQS	needwunsQS
needwunsQS,character,character-method	needwunsQS
needwunsQS,character,XString-method	needwunsQS
needwunsQS,XString,character-method	needwunsQS
needwunsQS,XString,XString-method	needwunsQS
nindel	AlignedXStringSet-class
nindel,AlignedXStringSet-method	AlignedXStringSet-class
nindel,PairwiseAlignedFixedSubject-method	PairwiseAlignedFixedSubject-class
nindel,PairwiseAlignedFixedSubjectSummary-method	PairwiseAlignedFixedSubject-class
nmatch	match-utils
nmatch,ANY,XStringViews-method	match-utils
nmatch,PairwiseAlignedFixedSubject,missing-method	align-utils
nmatch,PairwiseAlignedFixedSubjectSummary,missing-method	align-utils
nmismatch	match-utils
nmismatch,AlignedXStringSet,missing-method	align-utils
nmismatch,ANY,XStringViews-method	match-utils
nmismatch,PairwiseAlignedFixedSubject,missing-method	align-utils
nmismatch,PairwiseAlignedFixedSubjectSummary,missing-method	align-utils
nmismatchEndingAt	match-utils
nmismatchStartingAt	match-utils
nucleotideSubstitutionMatrix	substitution_matrices
oligonucleotideFrequency	alphabetFrequency
oligonucleotideFrequency,DNAString-method	alphabetFrequency
oligonucleotideFrequency,MaskedXString-method	alphabetFrequency
oligonucleotideFrequency,RNAString-method	alphabetFrequency
oligonucleotideFrequency,XStringSet-method	alphabetFrequency
oligonucleotideFrequency,XStringViews-method	alphabetFrequency
oligonucleotideTransitions	alphabetFrequency
order	XStringSet-class
order,XStringSet-method	XStringSet-class
PairwiseAlignedFixedSubject	PairwiseAlignedFixedSubject-class
PairwiseAlignedFixedSubject-class	PairwiseAlignedFixedSubject-class
PairwiseAlignedFixedSubjectSummary	PairwiseAlignedFixedSubject-class
PairwiseAlignedFixedSubjectSummary-class	PairwiseAlignedFixedSubject-class
pairwiseAlignment	pairwiseAlignment
pairwiseAlignment,character,character-method	pairwiseAlignment
pairwiseAlignment,character,QualityScaledXStringSet-method	pairwiseAlignment
pairwiseAlignment,character,XString-method	pairwiseAlignment
pairwiseAlignment,character,XStringSet-method	pairwiseAlignment
pairwiseAlignment,QualityScaledXStringSet,character-method	pairwiseAlignment
pairwiseAlignment,QualityScaledXStringSet,QualityScaledXStringSet-method	pairwiseAlignment
pairwiseAlignment,QualityScaledXStringSet,XString-method	pairwiseAlignment
pairwiseAlignment,QualityScaledXStringSet,XStringSet-method	pairwiseAlignment
pairwiseAlignment,XString,character-method	pairwiseAlignment
pairwiseAlignment,XString,QualityScaledXStringSet-method	pairwiseAlignment
pairwiseAlignment,XString,XString-method	pairwiseAlignment
pairwiseAlignment,XString,XStringSet-method	pairwiseAlignment
pairwiseAlignment,XStringSet,character-method	pairwiseAlignment
pairwiseAlignment,XStringSet,QualityScaledXStringSet-method	pairwiseAlignment
pairwiseAlignment,XStringSet,XString-method	pairwiseAlignment
pairwiseAlignment,XStringSet,XStringSet-method	pairwiseAlignment
palindromeArmLength	findPalindromes
palindromeArmLength,XString-method	findPalindromes
palindromeArmLength,XStringViews-method	findPalindromes
palindromeLeftArm	findPalindromes
palindromeLeftArm,XString-method	findPalindromes
palindromeLeftArm,XStringViews-method	findPalindromes
palindromeRightArm	findPalindromes
palindromeRightArm,XString-method	findPalindromes
palindromeRightArm,XStringViews-method	findPalindromes
PAM120	substitution_matrices
PAM250	substitution_matrices
PAM30	substitution_matrices
PAM40	substitution_matrices
PAM70	substitution_matrices
pattern	XStringPartialMatches-class
pattern,PairwiseAlignedFixedSubject-method	PairwiseAlignedFixedSubject-class
pattern,XStringPartialMatches-method	XStringPartialMatches-class
patternFrequency	PDict-class
patternFrequency,PDict-method	PDict-class
PDict	PDict-class
PDict,AsIs-method	PDict-class
PDict,character-method	PDict-class
PDict,DNAStringSet-method	PDict-class
PDict,XStringViews-method	PDict-class
PDict-class	PDict-class
PDict3Parts	PDict-class
PDict3Parts-class	PDict-class
phiX174Phage	phiX174Phage
PhredQuality	XStringQuality-class
PhredQuality-class	XStringQuality-class
pid	pid
pid,PairwiseAlignedFixedSubject-method	pid
pmatchPattern	pmatchPattern
pmatchPattern,character-method	pmatchPattern
pmatchPattern,XString-method	pmatchPattern
pmatchPattern,XStringViews-method	pmatchPattern
PreprocessedTB	PDict-class
PreprocessedTB-class	PDict-class
print.needwunsQS	needwunsQS
PWMscore	matchPWM
quality	QualityScaledXStringSet-class
quality,QualityScaledXStringSet-method	QualityScaledXStringSet-class
QualityAlignedXStringSet	AlignedXStringSet-class
QualityAlignedXStringSet-class	AlignedXStringSet-class
QualityScaledAAStringSet	QualityScaledXStringSet-class
QualityScaledAAStringSet-class	QualityScaledXStringSet-class
QualityScaledBStringSet	QualityScaledXStringSet-class
QualityScaledBStringSet-class	QualityScaledXStringSet-class
QualityScaledDNAStringSet	QualityScaledXStringSet-class
QualityScaledDNAStringSet-class	QualityScaledXStringSet-class
QualityScaledRNAStringSet	QualityScaledXStringSet-class
QualityScaledRNAStringSet-class	QualityScaledXStringSet-class
QualityScaledXStringSet	QualityScaledXStringSet-class
QualityScaledXStringSet-class	QualityScaledXStringSet-class
qualitySubstitutionMatrices	substitution_matrices
quPhiX174	phiX174Phage
read.AAStringSet	XStringSet-io
read.BStringSet	XStringSet-io
read.BStringViews	XStringSet-io
read.DNAStringSet	XStringSet-io
read.RNAStringSet	XStringSet-io
read.XStringViews	XStringSet-io
readFASTA	readFASTA
reduce,MaskedXString-method	MaskedXString-class
rep,AlignedXStringSet-method	AlignedXStringSet-class
rep,PairwiseAlignedFixedSubject-method	PairwiseAlignedFixedSubject-class
rep,XStringSet-method	XStringSet-class
replaceLetterAt	replaceLetterAt
replaceLetterAt,DNAString-method	replaceLetterAt
replaceLetterAtLoc	replaceLetterAt
reverse,MaskedXString-method	reverse
reverse,XString-method	reverse
reverse,XStringSet-method	reverse
reverse,XStringViews-method	reverse
reverseComplement	reverse
reverseComplement,DNAString-method	reverse
reverseComplement,DNAStringSet-method	reverse
reverseComplement,MaskedDNAString-method	reverse
reverseComplement,MaskedRNAString-method	reverse
reverseComplement,matrix-method	matchPWM
reverseComplement,RNAString-method	reverse
reverseComplement,RNAStringSet-method	reverse
reverseComplement,XStringViews-method	reverse
rna2dna	translate
RNAString	RNAString-class
RNAString-class	RNAString-class
RNAStringSet	XStringSet-class
RNAStringSet-class	XStringSet-class
RNA_ALPHABET	RNAString-class
RNA_BASES	RNAString-class
RNA_GENETIC_CODE	GENETIC_CODE
score	PairwiseAlignedFixedSubject-class
score,PairwiseAlignedFixedSubject-method	PairwiseAlignedFixedSubject-class
score,PairwiseAlignedFixedSubjectSummary-method	PairwiseAlignedFixedSubject-class
show,ACtree-method	PDict-class
show,ACtree2-method	PDict-class
show,AlignedXStringSet-method	AlignedXStringSet-class
show,ByPos_MIndex-method	MIndex-class
show,Dups-method	Biostrings-internals
show,MaskedXString-method	MaskedXString-class
show,MTB_PDict-method	PDict-class
show,PairwiseAlignedFixedSubject-method	PairwiseAlignedFixedSubject-class
show,PairwiseAlignedFixedSubjectSummary-method	PairwiseAlignedFixedSubject-class
show,QualityScaledXStringSet-method	QualityScaledXStringSet-class
show,TB_PDict-method	PDict-class
show,Twobit-method	PDict-class
show,XString-method	XString-class
show,XStringPartialMatches-method	XStringPartialMatches-class
show,XStringSet-method	XStringSet-class
show,XStringViews-method	XStringViews-class
SolexaQuality	XStringQuality-class
SolexaQuality-class	XStringQuality-class
sort,XStringSet-method	XStringSet-class
SparseList	Biostrings-internals
SparseList-class	Biostrings-internals
srPhiX174	phiX174Phage
start,AlignedXStringSet-method	AlignedXStringSet-class
startIndex	MIndex-class
startIndex,ByPos_MIndex-method	MIndex-class
stringDist	stringDist
stringDist,character-method	stringDist
stringDist,QualityScaledXStringSet-method	stringDist
stringDist,XStringSet-method	stringDist
strrev	alphabetFrequency
subBString	subXString
subject,PairwiseAlignedFixedSubject-method	PairwiseAlignedFixedSubject-class
subpatterns	XStringPartialMatches-class
subpatterns,XStringPartialMatches-method	XStringPartialMatches-class
subseq,MaskedXString-method	MaskedXString-class
substitution.matrices	substitution_matrices
substr	subXString
substr,MaskedXString-method	subXString
substr,XString-method	subXString
substring	subXString
substring,MaskedXString-method	subXString
substring,XString-method	subXString
subXString	subXString
summary,PairwiseAlignedFixedSubject-method	PairwiseAlignedFixedSubject-class
tail,PDict3Parts-method	PDict-class
tail,TB_PDict-method	PDict-class
tb	PDict-class
tb,PDict3Parts-method	PDict-class
tb,PreprocessedTB-method	PDict-class
tb,TB_PDict-method	PDict-class
tb.width	PDict-class
tb.width,PDict3Parts-method	PDict-class
tb.width,PreprocessedTB-method	PDict-class
tb.width,TB_PDict-method	PDict-class
TB_PDict	PDict-class
TB_PDict-class	PDict-class
toComplex	toComplex
toComplex,DNAString-method	toComplex
toString,AlignedXStringSet-method	AlignedXStringSet-class
toString,MaskedXString-method	MaskedXString-class
toString,PairwiseAlignedFixedSubject-method	PairwiseAlignedFixedSubject-class
toString,XString-method	XString-class
toString,XStringSet-method	XStringSet-class
toString,XStringViews-method	XStringViews-class
transcribe	translate
translate	translate
translate,DNAString-method	translate
translate,DNAStringSet-method	translate
translate,MaskedDNAString-method	translate
translate,MaskedRNAString-method	translate
translate,RNAString-method	translate
translate,RNAStringSet-method	translate
trinucleotideFrequency	alphabetFrequency
Twobit	PDict-class
Twobit-class	PDict-class
type	PairwiseAlignedFixedSubject-class
type,PairwiseAlignedFixedSubject-method	PairwiseAlignedFixedSubject-class
type,PairwiseAlignedFixedSubjectSummary-method	PairwiseAlignedFixedSubject-class
unaligned	AlignedXStringSet-class
unaligned,AlignedXStringSet-method	AlignedXStringSet-class
uniqueLetters	alphabetFrequency
uniqueLetters,MaskedXString-method	alphabetFrequency
uniqueLetters,XString-method	alphabetFrequency
uniqueLetters,XStringSet-method	alphabetFrequency
uniqueLetters,XStringViews-method	alphabetFrequency
unlist,MIndex-method	MIndex-class
unmasked	MaskedXString-class
unmasked,MaskedXString-method	MaskedXString-class
vcountPattern	matchPattern
vcountPattern,character-method	matchPattern
vcountPattern,MaskedXString-method	matchPattern
vcountPattern,XString-method	matchPattern
vcountPattern,XStringSet-method	matchPattern
vcountPattern,XStringViews-method	matchPattern
vcountPDict	matchPDict-exact
vcountPDict,MaskedXString-method	matchPDict-exact
vcountPDict,XString-method	matchPDict-exact
vcountPDict,XStringSet-method	matchPDict-exact
vcountPDict,XStringViews-method	matchPDict-exact
Views,character-method	XStringViews-class
Views,MaskedXString-method	MaskedXString-class
Views,PairwiseAlignedFixedSubject-method	PairwiseAlignedFixedSubject-class
Views,XString-method	XStringViews-class
vmatchPattern	matchPattern
vmatchPattern,character-method	matchPattern
vmatchPattern,MaskedXString-method	matchPattern
vmatchPattern,XString-method	matchPattern
vmatchPattern,XStringSet-method	matchPattern
vmatchPattern,XStringViews-method	matchPattern
vmatchPDict	matchPDict-exact
vmatchPDict,ANY-method	matchPDict-exact
vmatchPDict,MaskedXString-method	matchPDict-exact
vmatchPDict,XString-method	matchPDict-exact
whichPDict	matchPDict-exact
whichPDict,XString-method	matchPDict-exact
width,AlignedXStringSet-method	AlignedXStringSet-class
width,PDict-method	PDict-class
width,PDict3Parts-method	PDict-class
width,PreprocessedTB-method	PDict-class
width,XStringSet-method	XStringSet-class
write.BStringViews	XStringSet-io
write.XStringSet	XStringSet-io
write.XStringViews	XStringSet-io
writeFASTA	readFASTA
wtPhiX174	phiX174Phage
XString	XString-class
XString,AsIs-method	XString-class
XString,character-method	XString-class
XString,MaskedXString-method	MaskedXString-class
XString,XString-method	XString-class
XString-class	XString-class
XStringCodec	Biostrings-internals
XStringCodec-class	Biostrings-internals
XStringPartialMatches-class	XStringPartialMatches-class
XStringQuality	XStringQuality-class
XStringQuality-class	XStringQuality-class
XStringSet	XStringSet-class
XStringSet,AsIs-method	XStringSet-class
XStringSet,character-method	XStringSet-class
XStringSet,XString-method	XStringSet-class
XStringSet,XStringSet-method	XStringSet-class
XStringSet,XStringViews-method	XStringSet-class
XStringSet-class	XStringSet-class
XStringSetToFASTArecords	XStringSet-io
XStringViews	XStringViews-constructors
XStringViews,ANY-method	XStringViews-constructors
XStringViews,XString-method	XStringViews-constructors
XStringViews,XStringViews-method	XStringViews-constructors
XStringViews-class	XStringViews-class
XStringViews-constructors	XStringViews-constructors
yeastSEQCHR1	yeastSEQCHR1
[,ACtree,ANY,ANY,ANY-method	PDict-class
[,AlignedXStringSet,ANY,ANY,ANY-method	AlignedXStringSet-class
[,PairwiseAlignedFixedSubject,ANY,ANY,ANY-method	PairwiseAlignedFixedSubject-class
[,QualityAlignedXStringSet,ANY,ANY,ANY-method	AlignedXStringSet-class
[,QualityScaledXStringSet,ANY,ANY,ANY-method	QualityScaledXStringSet-class
[,XString,ANY,ANY,ANY-method	XString-class
[,XStringPartialMatches,ANY,ANY,ANY-method	XStringPartialMatches-class
[,XStringSet,ANY,ANY,ANY-method	XStringSet-class
[<-,AlignedXStringSet,ANY,ANY,ANY-method	AlignedXStringSet-class
[<-,PairwiseAlignedFixedSubject,ANY,ANY,ANY-method	PairwiseAlignedFixedSubject-class
[[,ByPos_MIndex-method	MIndex-class
[[,PDict-method	PDict-class
[[,SparseList-method	Biostrings-internals
[[,XStringSet-method	XStringSet-class
[[<-,XStringSet-method	XStringSet-class
