!=,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
AAMultipleAlignment	MultipleAlignment-class
AAMultipleAlignment-class	MultipleAlignment-class
AAString	AAString-class
AAString-class	AAString-class
AAStringSet	XStringSet-class
AAStringSet-class	XStringSet-class
AAStringSetList	XStringSetList-class
AAStringSetList-class	XStringSetList-class
AA_ALPHABET	AAString-class
AA_PROTEINOGENIC	AAString-class
AA_STANDARD	AAString-class
ACtree2	PDict-class
ACtree2-class	PDict-class
align-utils	align-utils
aligned	AlignedXStringSet-class
aligned,AlignedXStringSet0-method	AlignedXStringSet-class
aligned,PairwiseAlignmentsSingleSubject-method	PairwiseAlignments-class
alignedPattern	PairwiseAlignments-class
alignedPattern,PairwiseAlignments-method	PairwiseAlignments-class
alignedSubject	PairwiseAlignments-class
alignedSubject,PairwiseAlignments-method	PairwiseAlignments-class
AlignedXStringSet	AlignedXStringSet-class
AlignedXStringSet-class	AlignedXStringSet-class
AlignedXStringSet0	AlignedXStringSet-class
AlignedXStringSet0-class	AlignedXStringSet-class
alphabet	XString-class
alphabet,ANY-method	XString-class
alphabet,XStringQuality-method	XStringQuality-class
alphabetFrequency	letterFrequency
alphabetFrequency,AAString-method	letterFrequency
alphabetFrequency,AAStringSet-method	letterFrequency
alphabetFrequency,DNAString-method	letterFrequency
alphabetFrequency,DNAStringSet-method	letterFrequency
alphabetFrequency,MaskedXString-method	letterFrequency
alphabetFrequency,MultipleAlignment-method	MultipleAlignment-class
alphabetFrequency,RNAString-method	letterFrequency
alphabetFrequency,RNAStringSet-method	letterFrequency
alphabetFrequency,XString-method	letterFrequency
alphabetFrequency,XStringSet-method	letterFrequency
alphabetFrequency,XStringViews-method	letterFrequency
AMINO_ACID_CODE	AMINO_ACID_CODE
anyNA,XStringSet-method	XStringSet-comparison
as.character,AlignedXStringSet0-method	AlignedXStringSet-class
as.character,MaskedXString-method	MaskedXString-class
as.character,MultipleAlignment-method	MultipleAlignment-class
as.character,PairwiseAlignmentsSingleSubject-method	PairwiseAlignments-class
as.character,XString-method	XString-class
as.character,XStringSet-method	XStringSet-class
as.character,XStringViews-method	XStringViews-class
as.data.frame,XStringSet-method	XStringSet-class
as.data.frame,XStringViews-method	XStringViews-class
as.factor,XStringSet-method	XStringSet-class
as.list,MTB_PDict-method	PDict-class
as.list,SparseList-method	Biostrings-internals
as.matrix,MultipleAlignment-method	MultipleAlignment-class
as.matrix,PairwiseAlignmentsSingleSubject-method	PairwiseAlignments-class
as.matrix,XStringQuality-method	XStringQuality-class
as.matrix,XStringSet-method	XStringSet-class
as.matrix,XStringViews-method	XStringViews-class
as.vector,XString-method	XString-class
as.vector,XStringQuality-method	XStringQuality-class
as.vector,XStringSet-method	XStringSet-class
BLOSUM100	substitution_matrices
BLOSUM45	substitution_matrices
BLOSUM50	substitution_matrices
BLOSUM62	substitution_matrices
BLOSUM80	substitution_matrices
BString	XString-class
BString-class	XString-class
BStringSet	XStringSet-class
BStringSet-class	XStringSet-class
BStringSetList	XStringSetList-class
BStringSetList-class	XStringSetList-class
ByPos_MIndex-class	MIndex-class
chartr	chartr
chartr,ANY,ANY,MaskedXString-method	chartr
chartr,ANY,ANY,XString-method	chartr
chartr,ANY,ANY,XStringSet-method	chartr
chartr,ANY,ANY,XStringViews-method	chartr
class:AAMultipleAlignment	MultipleAlignment-class
class:AAString	AAString-class
class:AAStringSet	XStringSet-class
class:AAStringSetList	XStringSetList-class
class:ACtree2	PDict-class
class:AlignedXStringSet	AlignedXStringSet-class
class:AlignedXStringSet0	AlignedXStringSet-class
class:BString	XString-class
class:BStringSet	XStringSet-class
class:BStringSetList	XStringSetList-class
class:ByPos_MIndex	MIndex-class
class:DNAMultipleAlignment	MultipleAlignment-class
class:DNAString	DNAString-class
class:DNAStringSet	XStringSet-class
class:DNAStringSetList	XStringSetList-class
class:Expanded_TB_PDict	PDict-class
class:IlluminaQuality	XStringQuality-class
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:MultipleAlignment	MultipleAlignment-class
class:PairwiseAlignments	PairwiseAlignments-class
class:PairwiseAlignmentsSingleSubject	PairwiseAlignments-class
class:PairwiseAlignmentsSingleSubjectSummary	PairwiseAlignments-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:RNAMultipleAlignment	MultipleAlignment-class
class:RNAString	RNAString-class
class:RNAStringSet	XStringSet-class
class:RNAStringSetList	XStringSetList-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:XStringSetList	XStringSetList-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,ANY,AAStringSet-method	XStringSet-class
coerce,ANY,BStringSet-method	XStringSet-class
coerce,ANY,DNAStringSet-method	XStringSet-class
coerce,ANY,RNAStringSet-method	XStringSet-class
coerce,ANY,XStringSet-method	XStringSet-class
coerce,BString,IlluminaQuality-method	XStringQuality-class
coerce,BString,MaskedBString-method	MaskedXString-class
coerce,BString,PhredQuality-method	XStringQuality-class
coerce,BString,SolexaQuality-method	XStringQuality-class
coerce,BStringSet,IlluminaQuality-method	XStringQuality-class
coerce,BStringSet,PhredQuality-method	XStringQuality-class
coerce,BStringSet,SolexaQuality-method	XStringQuality-class
coerce,character,AAMultipleAlignment-method	MultipleAlignment-class
coerce,character,AAString-method	XString-class
coerce,character,BString-method	XString-class
coerce,character,DNAMultipleAlignment-method	MultipleAlignment-class
coerce,character,DNAString-method	XString-class
coerce,character,IlluminaQuality-method	XStringQuality-class
coerce,character,PhredQuality-method	XStringQuality-class
coerce,character,RNAMultipleAlignment-method	MultipleAlignment-class
coerce,character,RNAString-method	XString-class
coerce,character,SolexaQuality-method	XStringQuality-class
coerce,character,XString-method	XString-class
coerce,DNAString,MaskedDNAString-method	MaskedXString-class
coerce,integer,IlluminaQuality-method	XStringQuality-class
coerce,integer,PhredQuality-method	XStringQuality-class
coerce,integer,SolexaQuality-method	XStringQuality-class
coerce,IntegerList,IlluminaQuality-method	XStringQuality-class
coerce,IntegerList,PhredQuality-method	XStringQuality-class
coerce,IntegerList,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,MaskedAAString-method	MaskedXString-class
coerce,MaskedXString,MaskedBString-method	MaskedXString-class
coerce,MaskedXString,MaskedDNAString-method	MaskedXString-class
coerce,MaskedXString,MaskedRNAString-method	MaskedXString-class
coerce,MaskedXString,NormalIRanges-method	MaskedXString-class
coerce,MaskedXString,Views-method	MaskedXString-class
coerce,MaskedXString,XStringViews-method	MaskedXString-class
coerce,MIndex,CompressedIRangesList-method	MIndex-class
coerce,MultipleAlignment,AAStringSet-method	MultipleAlignment-class
coerce,MultipleAlignment,BStringSet-method	MultipleAlignment-class
coerce,MultipleAlignment,DNAStringSet-method	MultipleAlignment-class
coerce,MultipleAlignment,RNAStringSet-method	MultipleAlignment-class
coerce,numeric,IlluminaQuality-method	XStringQuality-class
coerce,numeric,PhredQuality-method	XStringQuality-class
coerce,numeric,SolexaQuality-method	XStringQuality-class
coerce,NumericList,IlluminaQuality-method	XStringQuality-class
coerce,NumericList,PhredQuality-method	XStringQuality-class
coerce,NumericList,SolexaQuality-method	XStringQuality-class
coerce,RNAString,MaskedRNAString-method	MaskedXString-class
coerce,XString,AAString-method	XString-class
coerce,XString,BString-method	XString-class
coerce,XString,DNAString-method	XString-class
coerce,XString,RNAString-method	XString-class
coerce,XStringQuality,IntegerList-method	XStringQuality-class
coerce,XStringQuality,matrix-method	XStringQuality-class
coerce,XStringQuality,NumericList-method	XStringQuality-class
coerce,XStringSet,Views-method	XStringViews-class
coerce,XStringSet,XStringViews-method	XStringViews-class
coerce,XStringViews,AAStringSet-method	XStringViews-class
coerce,XStringViews,BStringSet-method	XStringViews-class
coerce,XStringViews,DNAStringSet-method	XStringViews-class
coerce,XStringViews,RNAStringSet-method	XStringViews-class
coerce,XStringViews,XStringSet-method	XStringViews-class
collapse,MaskedXString-method	MaskedXString-class
colmask	MultipleAlignment-class
colmask,MultipleAlignment-method	MultipleAlignment-class
colmask<-	MultipleAlignment-class
colmask<-,MultipleAlignment,ANY-method	MultipleAlignment-class
colmask<-,MultipleAlignment,NULL-method	MultipleAlignment-class
compareStrings	align-utils
compareStrings,AlignedXStringSet0,AlignedXStringSet0-method	align-utils
compareStrings,character,character-method	align-utils
compareStrings,PairwiseAlignments,missing-method	align-utils
compareStrings,XString,XString-method	align-utils
compareStrings,XStringSet,XStringSet-method	align-utils
complement	reverseComplement
complement,DNAString-method	reverseComplement
complement,DNAStringSet-method	reverseComplement
complement,MaskedDNAString-method	reverseComplement
complement,MaskedRNAString-method	reverseComplement
complement,RNAString-method	reverseComplement
complement,RNAStringSet-method	reverseComplement
complement,XStringViews-method	reverseComplement
computeAllFlinks	PDict-class
computeAllFlinks,ACtree2-method	PDict-class
consensusMatrix	letterFrequency
consensusMatrix,character-method	letterFrequency
consensusMatrix,matrix-method	letterFrequency
consensusMatrix,MultipleAlignment-method	MultipleAlignment-class
consensusMatrix,PairwiseAlignmentsSingleSubject-method	align-utils
consensusMatrix,XStringSet-method	letterFrequency
consensusMatrix,XStringViews-method	letterFrequency
consensusString	letterFrequency
consensusString,AAMultipleAlignment-method	MultipleAlignment-class
consensusString,ANY-method	letterFrequency
consensusString,BStringSet-method	letterFrequency
consensusString,DNAMultipleAlignment-method	MultipleAlignment-class
consensusString,DNAStringSet-method	letterFrequency
consensusString,matrix-method	letterFrequency
consensusString,MultipleAlignment-method	MultipleAlignment-class
consensusString,RNAMultipleAlignment-method	MultipleAlignment-class
consensusString,RNAStringSet-method	letterFrequency
consensusString,XStringViews-method	letterFrequency
consensusViews	MultipleAlignment-class
consensusViews,AAMultipleAlignment-method	MultipleAlignment-class
consensusViews,DNAMultipleAlignment-method	MultipleAlignment-class
consensusViews,MultipleAlignment-method	MultipleAlignment-class
consensusViews,RNAMultipleAlignment-method	MultipleAlignment-class
countPattern	matchPattern
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
countPWM,character-method	matchPWM
countPWM,DNAString-method	matchPWM
countPWM,MaskedDNAString-method	matchPWM
countPWM,XStringViews-method	matchPWM
coverage,AlignedXStringSet0-method	align-utils
coverage,MaskedXString-method	match-utils
coverage,MIndex-method	match-utils
coverage,PairwiseAlignmentsSingleSubject-method	align-utils
coverage,PairwiseAlignmentsSingleSubjectSummary-method	align-utils
deletion	InDel-class
deletion,InDel-method	InDel-class
deletion,PairwiseAlignments-method	PairwiseAlignments-class
detail	detail
detail,MultipleAlignment-method	MultipleAlignment-class
dim,MultipleAlignment-method	MultipleAlignment-class
dinucleotideFrequency	nucleotideFrequency
dinucleotideFrequencyTest	dinucleotideFrequencyTest
dinucleotideFrequencyTest,DNAStringSet-method	dinucleotideFrequencyTest
dinucleotideFrequencyTest,RNAStringSet-method	dinucleotideFrequencyTest
DNAMultipleAlignment	MultipleAlignment-class
DNAMultipleAlignment-class	MultipleAlignment-class
DNAString	DNAString-class
DNAString-class	DNAString-class
DNAStringSet	XStringSet-class
DNAStringSet-class	XStringSet-class
DNAStringSetList	XStringSetList-class
DNAStringSetList-class	XStringSetList-class
DNA_ALPHABET	DNAString-class
DNA_BASES	DNAString-class
duplicated,PDict-method	PDict-class
duplicated,PreprocessedTB-method	PDict-class
elementNROWS,MIndex-method	MIndex-class
encoding	XStringQuality-class
encoding,XStringQuality-method	XStringQuality-class
end,AlignedXStringSet0-method	AlignedXStringSet-class
endIndex	MIndex-class
endIndex,ByPos_MIndex-method	MIndex-class
errorSubstitutionMatrices	substitution_matrices
Expanded_TB_PDict	PDict-class
Expanded_TB_PDict-class	PDict-class
extractAllMatches	matchPDict-exact
extractAt	replaceAt
extractAt,XString-method	replaceAt
extractAt,XStringSet-method	replaceAt
fasta.index	XStringSet-io
fasta.seqlengths	XStringSet-io
fastq.geometry	XStringSet-io
fastq.seqlengths	XStringSet-io
findPalindromes	findPalindromes
findPalindromes,DNAString-method	findPalindromes
findPalindromes,MaskedXString-method	findPalindromes
findPalindromes,RNAString-method	findPalindromes
findPalindromes,XString-method	findPalindromes
findPalindromes,XStringViews-method	findPalindromes
gaps,MaskedXString-method	MaskedXString-class
GENETIC_CODE	GENETIC_CODE
GENETIC_CODE_TABLE	GENETIC_CODE
getGeneticCode	GENETIC_CODE
getSeq	getSeq
get_seqtype_conversion_lookup	Biostrings-internals
gregexpr2	gregexpr2
hasAllFlinks	PDict-class
hasAllFlinks,ACtree2-method	PDict-class
hasLetterAt	lowlevel-matching
hasOnlyBaseLetters	letterFrequency
hasOnlyBaseLetters,DNAString-method	letterFrequency
hasOnlyBaseLetters,DNAStringSet-method	letterFrequency
hasOnlyBaseLetters,MaskedXString-method	letterFrequency
hasOnlyBaseLetters,RNAString-method	letterFrequency
hasOnlyBaseLetters,RNAStringSet-method	letterFrequency
hasOnlyBaseLetters,XStringViews-method	letterFrequency
head,PDict3Parts-method	PDict-class
head,TB_PDict-method	PDict-class
HNF4alpha	HNF4alpha
IlluminaQuality	XStringQuality-class
IlluminaQuality-class	XStringQuality-class
InDel	InDel-class
indel	AlignedXStringSet-class
indel,AlignedXStringSet0-method	AlignedXStringSet-class
indel,PairwiseAlignments-method	PairwiseAlignments-class
InDel-class	InDel-class
initialize,ACtree2-method	PDict-class
initialize,PreprocessedTB-method	PDict-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
insertion,PairwiseAlignments-method	PairwiseAlignments-class
is.na,XStringSet-method	XStringSet-comparison
isMatchingAt	lowlevel-matching
isMatchingEndingAt	lowlevel-matching
isMatchingEndingAt,character-method	lowlevel-matching
isMatchingEndingAt,XString-method	lowlevel-matching
isMatchingEndingAt,XStringSet-method	lowlevel-matching
isMatchingStartingAt	lowlevel-matching
isMatchingStartingAt,character-method	lowlevel-matching
isMatchingStartingAt,XString-method	lowlevel-matching
isMatchingStartingAt,XStringSet-method	lowlevel-matching
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,MaskedXString-method	MaskedXString-class
length,MIndex-method	MIndex-class
length,PairwiseAlignmentsSingleSubjectSummary-method	PairwiseAlignments-class
length,PDict-method	PDict-class
length,PDict3Parts-method	PDict-class
length,PreprocessedTB-method	PDict-class
length,SparseList-method	Biostrings-internals
letter	letter
letter,character-method	letter
letter,MaskedXString-method	letter
letter,XString-method	letter
letter,XStringViews-method	letter
letterFrequency	letterFrequency
letterFrequency,MaskedXString-method	letterFrequency
letterFrequency,XString-method	letterFrequency
letterFrequency,XStringSet-method	letterFrequency
letterFrequency,XStringViews-method	letterFrequency
letterFrequencyInSlidingView	letterFrequency
letterFrequencyInSlidingView,XString-method	letterFrequency
longestConsecutive	longestConsecutive
lowlevel-matching	lowlevel-matching
mask	maskMotif
MaskedAAString	MaskedXString-class
MaskedAAString-class	MaskedXString-class
MaskedBString	MaskedXString-class
MaskedBString-class	MaskedXString-class
maskeddim	MultipleAlignment-class
maskeddim,MultipleAlignment-method	MultipleAlignment-class
MaskedDNAString	MaskedXString-class
MaskedDNAString-class	MaskedXString-class
maskedncol	MultipleAlignment-class
maskedncol,MultipleAlignment-method	MultipleAlignment-class
maskednrow	MultipleAlignment-class
maskednrow,MultipleAlignment-method	MultipleAlignment-class
maskedratio,MaskedXString-method	MaskedXString-class
maskedratio,MultipleAlignment-method	MultipleAlignment-class
MaskedRNAString	MaskedXString-class
MaskedRNAString-class	MaskedXString-class
maskedwidth,MaskedXString-method	MaskedXString-class
MaskedXString	MaskedXString-class
MaskedXString-class	MaskedXString-class
maskGaps	MultipleAlignment-class
maskGaps,MultipleAlignment-method	MultipleAlignment-class
maskMotif	maskMotif
maskMotif,MaskedXString,character-method	maskMotif
maskMotif,MaskedXString,XString-method	maskMotif
maskMotif,MultipleAlignment,ANY-method	MultipleAlignment-class
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,ANY,XStringSet-method	XStringSet-comparison
match,XStringSet,ANY-method	XStringSet-comparison
match,XStringSet,XStringSet-method	XStringSet-comparison
match-utils	match-utils
matchLRPatterns	matchLRPatterns
matchLRPatterns,MaskedXString-method	matchLRPatterns
matchLRPatterns,XString-method	matchLRPatterns
matchLRPatterns,XStringViews-method	matchLRPatterns
matchPattern	matchPattern
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
matchprobes	matchprobes
matchPWM	matchPWM
matchPWM,character-method	matchPWM
matchPWM,DNAString-method	matchPWM
matchPWM,MaskedDNAString-method	matchPWM
matchPWM,XStringViews-method	matchPWM
maxScore	matchPWM
maxScore,ANY-method	matchPWM
maxWeights	matchPWM
maxWeights,matrix-method	matchPWM
mergeIUPACLetters	IUPAC_CODE_MAP
MIndex	MIndex-class
MIndex-class	MIndex-class
minScore	matchPWM
minScore,ANY-method	matchPWM
minWeights	matchPWM
minWeights,matrix-method	matchPWM
misc	misc
mismatch	match-utils
mismatch,AlignedXStringSet0,missing-method	align-utils
mismatch,ANY,XStringViews-method	match-utils
mismatchSummary	align-utils
mismatchSummary,AlignedXStringSet0-method	align-utils
mismatchSummary,PairwiseAlignmentsSingleSubject-method	align-utils
mismatchSummary,PairwiseAlignmentsSingleSubjectSummary-method	align-utils
mismatchSummary,QualityAlignedXStringSet-method	align-utils
mismatchTable	align-utils
mismatchTable,AlignedXStringSet0-method	align-utils
mismatchTable,PairwiseAlignments-method	align-utils
mismatchTable,QualityAlignedXStringSet-method	align-utils
mkAllStrings	nucleotideFrequency
MTB_PDict	PDict-class
MTB_PDict-class	PDict-class
MultipleAlignment	MultipleAlignment-class
MultipleAlignment-class	MultipleAlignment-class
N50	misc
names,MIndex-method	MIndex-class
names,PDict-method	PDict-class
names<-,MIndex-method	MIndex-class
names<-,PDict-method	PDict-class
narrow,character-method	XStringSet-class
narrow,QualityScaledXStringSet-method	QualityScaledXStringSet-class
nchar,AlignedXStringSet0-method	AlignedXStringSet-class
nchar,MaskedXString-method	MaskedXString-class
nchar,MultipleAlignment-method	MultipleAlignment-class
nchar,PairwiseAlignments-method	PairwiseAlignments-class
nchar,PairwiseAlignmentsSingleSubjectSummary-method	PairwiseAlignments-class
nchar,XString-method	XString-class
nchar,XStringSet-method	XStringSet-class
nchar,XStringSetList-method	XStringSetList-class
nchar,XStringViews-method	XStringViews-class
ncol,MultipleAlignment-method	MultipleAlignment-class
nedit	align-utils
nedit,PairwiseAlignments-method	align-utils
nedit,PairwiseAlignmentsSingleSubjectSummary-method	align-utils
neditAt	lowlevel-matching
neditEndingAt	lowlevel-matching
neditEndingAt,character-method	lowlevel-matching
neditEndingAt,XString-method	lowlevel-matching
neditEndingAt,XStringSet-method	lowlevel-matching
neditStartingAt	lowlevel-matching
neditStartingAt,character-method	lowlevel-matching
neditStartingAt,XString-method	lowlevel-matching
neditStartingAt,XStringSet-method	lowlevel-matching
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,AlignedXStringSet0-method	AlignedXStringSet-class
nindel,PairwiseAlignments-method	PairwiseAlignments-class
nindel,PairwiseAlignmentsSingleSubjectSummary-method	PairwiseAlignments-class
nmatch	match-utils
nmatch,ANY,XStringViews-method	match-utils
nmatch,PairwiseAlignments,missing-method	align-utils
nmatch,PairwiseAlignmentsSingleSubjectSummary,missing-method	align-utils
nmismatch	match-utils
nmismatch,AlignedXStringSet0,missing-method	align-utils
nmismatch,ANY,XStringViews-method	match-utils
nmismatch,PairwiseAlignments,missing-method	align-utils
nmismatch,PairwiseAlignmentsSingleSubjectSummary,missing-method	align-utils
nnodes	PDict-class
nnodes,ACtree2-method	PDict-class
nrow,MultipleAlignment-method	MultipleAlignment-class
nucleotideFrequencyAt	nucleotideFrequency
nucleotideFrequencyAt,XStringSet-method	nucleotideFrequency
nucleotideFrequencyAt,XStringViews-method	nucleotideFrequency
nucleotideSubstitutionMatrix	substitution_matrices
oligonucleotideFrequency	nucleotideFrequency
oligonucleotideFrequency,MaskedXString-method	nucleotideFrequency
oligonucleotideFrequency,XString-method	nucleotideFrequency
oligonucleotideFrequency,XStringSet-method	nucleotideFrequency
oligonucleotideFrequency,XStringViews-method	nucleotideFrequency
oligonucleotideTransitions	nucleotideFrequency
padAndClip	padAndClip
pairwiseAlignment	pairwiseAlignment
pairwiseAlignment,ANY,ANY-method	pairwiseAlignment
pairwiseAlignment,ANY,QualityScaledXStringSet-method	pairwiseAlignment
pairwiseAlignment,QualityScaledXStringSet,ANY-method	pairwiseAlignment
pairwiseAlignment,QualityScaledXStringSet,QualityScaledXStringSet-method	pairwiseAlignment
PairwiseAlignments	PairwiseAlignments-class
PairwiseAlignments,character,character-method	PairwiseAlignments-class
PairwiseAlignments,character,missing-method	PairwiseAlignments-class
PairwiseAlignments,XString,XString-method	PairwiseAlignments-class
PairwiseAlignments,XStringSet,missing-method	PairwiseAlignments-class
PairwiseAlignments-class	PairwiseAlignments-class
PairwiseAlignments-io	PairwiseAlignments-io
PairwiseAlignmentsSingleSubject	PairwiseAlignments-class
PairwiseAlignmentsSingleSubject,character,character-method	PairwiseAlignments-class
PairwiseAlignmentsSingleSubject,character,missing-method	PairwiseAlignments-class
PairwiseAlignmentsSingleSubject,XString,XString-method	PairwiseAlignments-class
PairwiseAlignmentsSingleSubject,XStringSet,missing-method	PairwiseAlignments-class
PairwiseAlignmentsSingleSubject-class	PairwiseAlignments-class
PairwiseAlignmentsSingleSubjectSummary	PairwiseAlignments-class
PairwiseAlignmentsSingleSubjectSummary-class	PairwiseAlignments-class
palindromeArmLength	findPalindromes
palindromeArmLength,DNAString-method	findPalindromes
palindromeArmLength,RNAString-method	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
parallelSlotNames,AlignedXStringSet0-method	AlignedXStringSet-class
parallelSlotNames,PairwiseAlignments-method	PairwiseAlignments-class
parallelSlotNames,QualityScaledXStringSet-method	QualityScaledXStringSet-class
parallelVectorNames,AlignedXStringSet0-method	AlignedXStringSet-class
pattern	XStringPartialMatches-class
pattern,PairwiseAlignments-method	PairwiseAlignments-class
pattern,XStringPartialMatches-method	XStringPartialMatches-class
patternFrequency	PDict-class
patternFrequency,PDict-method	PDict-class
pcompare,ANY,XStringSet-method	XStringSet-comparison
pcompare,XStringSet,ANY-method	XStringSet-comparison
pcompare,XStringSet,XStringSet-method	XStringSet-comparison
PDict	PDict-class
PDict,AsIs-method	PDict-class
PDict,character-method	PDict-class
PDict,DNAStringSet-method	PDict-class
PDict,probetable-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,PairwiseAlignments-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
PWM	matchPWM
PWM,character-method	matchPWM
PWM,DNAStringSet-method	matchPWM
PWM,matrix-method	matchPWM
PWMscoreStartingAt	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
ranges,AlignedXStringSet0-method	AlignedXStringSet-class
readAAMultipleAlignment	MultipleAlignment-class
readAAStringSet	XStringSet-io
readBStringSet	XStringSet-io
readDNAMultipleAlignment	MultipleAlignment-class
readDNAStringSet	XStringSet-io
readQualityScaledDNAStringSet	QualityScaledXStringSet-class
readRNAMultipleAlignment	MultipleAlignment-class
readRNAStringSet	XStringSet-io
replaceAmbiguities	chartr
replaceAt	replaceAt
replaceAt,XString-method	replaceAt
replaceAt,XStringSet-method	replaceAt
replaceLetterAt	replaceLetterAt
replaceLetterAt,DNAString-method	replaceLetterAt
replaceLetterAt,DNAStringSet-method	replaceLetterAt
reverse,MaskedXString-method	reverseComplement
reverse,QualityScaledXStringSet-method	QualityScaledXStringSet-class
reverseComplement	reverseComplement
reverseComplement,DNAString-method	reverseComplement
reverseComplement,DNAStringSet-method	reverseComplement
reverseComplement,MaskedDNAString-method	reverseComplement
reverseComplement,MaskedRNAString-method	reverseComplement
reverseComplement,matrix-method	matchPWM
reverseComplement,QualityScaledDNAStringSet-method	QualityScaledXStringSet-class
reverseComplement,QualityScaledRNAStringSet-method	QualityScaledXStringSet-class
reverseComplement,RNAString-method	reverseComplement
reverseComplement,RNAStringSet-method	reverseComplement
reverseComplement,XStringViews-method	reverseComplement
RNAMultipleAlignment	MultipleAlignment-class
RNAMultipleAlignment-class	MultipleAlignment-class
RNAString	RNAString-class
RNAString-class	RNAString-class
RNAStringSet	XStringSet-class
RNAStringSet-class	XStringSet-class
RNAStringSetList	XStringSetList-class
RNAStringSetList-class	XStringSetList-class
RNA_ALPHABET	RNAString-class
RNA_BASES	RNAString-class
RNA_GENETIC_CODE	GENETIC_CODE
rowmask	MultipleAlignment-class
rowmask,MultipleAlignment-method	MultipleAlignment-class
rowmask<-	MultipleAlignment-class
rowmask<-,MultipleAlignment,ANY-method	MultipleAlignment-class
rowmask<-,MultipleAlignment,NULL-method	MultipleAlignment-class
rownames,MultipleAlignment-method	MultipleAlignment-class
rownames<-,MultipleAlignment-method	MultipleAlignment-class
saveXStringSet	XStringSet-io
score,PairwiseAlignments-method	PairwiseAlignments-class
score,PairwiseAlignmentsSingleSubjectSummary-method	PairwiseAlignments-class
seqtype	Biostrings-internals
seqtype,AAString-method	XString-class
seqtype,AlignedXStringSet0-method	AlignedXStringSet-class
seqtype,BString-method	XString-class
seqtype,DNAString-method	XString-class
seqtype,MaskedXString-method	MaskedXString-class
seqtype,MultipleAlignment-method	MultipleAlignment-class
seqtype,PairwiseAlignments-method	PairwiseAlignments-class
seqtype,RNAString-method	XString-class
seqtype,XStringSet-method	XStringSet-class
seqtype,XStringSetList-method	XStringSetList-class
seqtype,XStringViews-method	XStringViews-class
seqtype<-	Biostrings-internals
seqtype<-,MaskedXString-method	MaskedXString-class
seqtype<-,XString-method	XString-class
seqtype<-,XStringSet-method	XStringSet-class
seqtype<-,XStringSetList-method	XStringSetList-class
seqtype<-,XStringViews-method	XStringViews-class
show,ACtree2-method	PDict-class
show,AlignedXStringSet0-method	AlignedXStringSet-class
show,MaskedXString-method	MaskedXString-class
show,MIndex-method	MIndex-class
show,MTB_PDict-method	PDict-class
show,MultipleAlignment-method	MultipleAlignment-class
show,PairwiseAlignments-method	PairwiseAlignments-class
show,PairwiseAlignmentsSingleSubjectSummary-method	PairwiseAlignments-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,XStringSetList-method	XStringSetList-class
show,XStringViews-method	XStringViews-class
showAsCell,XString-method	XString-class
showAsCell,XStringSet-method	XStringSet-class
SolexaQuality	XStringQuality-class
SolexaQuality-class	XStringQuality-class
SparseList	Biostrings-internals
SparseList-class	Biostrings-internals
srPhiX174	phiX174Phage
stackStrings	padAndClip
start,AlignedXStringSet0-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
subject,PairwiseAlignments-method	PairwiseAlignments-class
subpatterns	XStringPartialMatches-class
subpatterns,XStringPartialMatches-method	XStringPartialMatches-class
subseq,character-method	XStringSet-class
subseq,MaskedXString-method	MaskedXString-class
subseq<-,character-method	XStringSet-class
subseq<-,XStringSet-method	XStringSet-class
substitution.matrices	substitution_matrices
substr,XString-method	XString-class
substring,XString-method	XString-class
summary,PairwiseAlignmentsSingleSubject-method	PairwiseAlignments-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
threebands,character-method	XStringSet-class
toComplex	toComplex
toComplex,DNAString-method	toComplex
toString,AlignedXStringSet0-method	AlignedXStringSet-class
toString,MaskedXString-method	MaskedXString-class
toString,PairwiseAlignmentsSingleSubject-method	PairwiseAlignments-class
toString,XString-method	XString-class
toString,XStringSet-method	XStringSet-class
toString,XStringViews-method	XStringViews-class
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
trimLRPatterns	trimLRPatterns
trimLRPatterns,character-method	trimLRPatterns
trimLRPatterns,XString-method	trimLRPatterns
trimLRPatterns,XStringSet-method	trimLRPatterns
trinucleotideFrequency	nucleotideFrequency
Twobit	PDict-class
Twobit-class	PDict-class
type	PairwiseAlignments-class
type,PairwiseAlignments-method	PairwiseAlignments-class
type,PairwiseAlignmentsSingleSubjectSummary-method	PairwiseAlignments-class
unaligned	AlignedXStringSet-class
unaligned,AlignedXStringSet0-method	AlignedXStringSet-class
uniqueLetters	letterFrequency
uniqueLetters,MaskedXString-method	letterFrequency
uniqueLetters,XString-method	letterFrequency
uniqueLetters,XStringSet-method	letterFrequency
uniqueLetters,XStringViews-method	letterFrequency
unitScale	matchPWM
unlist,MIndex-method	MIndex-class
unlist,XStringSet-method	XStringSet-class
unmasked	MaskedXString-class
unmasked,MaskedXString-method	MaskedXString-class
unmasked,MultipleAlignment-method	MultipleAlignment-class
unmasked,XString-method	MaskedXString-class
updateObject,XString-method	XString-class
updateObject,XStringSet-method	XStringSet-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,PairwiseAlignmentsSingleSubject-method	PairwiseAlignments-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
vwhichPDict	matchPDict-exact
vwhichPDict,MaskedXString-method	matchPDict-exact
vwhichPDict,XString-method	matchPDict-exact
vwhichPDict,XStringSet-method	matchPDict-exact
vwhichPDict,XStringViews-method	matchPDict-exact
which.isMatchingAt	lowlevel-matching
which.isMatchingEndingAt	lowlevel-matching
which.isMatchingEndingAt,character-method	lowlevel-matching
which.isMatchingEndingAt,XString-method	lowlevel-matching
which.isMatchingEndingAt,XStringSet-method	lowlevel-matching
which.isMatchingStartingAt	lowlevel-matching
which.isMatchingStartingAt,character-method	lowlevel-matching
which.isMatchingStartingAt,XString-method	lowlevel-matching
which.isMatchingStartingAt,XStringSet-method	lowlevel-matching
whichPDict	matchPDict-exact
whichPDict,MaskedXString-method	matchPDict-exact
whichPDict,XString-method	matchPDict-exact
whichPDict,XStringSet-method	matchPDict-exact
whichPDict,XStringViews-method	matchPDict-exact
width,AlignedXStringSet0-method	AlignedXStringSet-class
width,character-method	XStringSet-class
width,PDict-method	PDict-class
width,PDict3Parts-method	PDict-class
width,PreprocessedTB-method	PDict-class
width0	MIndex-class
width0,MIndex-method	MIndex-class
windows,character-method	XStringSet-class
windows,QualityScaledXStringSet-method	QualityScaledXStringSet-class
write.phylip	MultipleAlignment-class
writePairwiseAlignments	PairwiseAlignments-io
writeQualityScaledXStringSet	QualityScaledXStringSet-class
writeXStringSet	XStringSet-io
wtPhiX174	phiX174Phage
xscat	xscat
XString	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-class	XStringSet-class
XStringSet-comparison	XStringSet-comparison
XStringSet-io	XStringSet-io
XStringSetList	XStringSetList-class
XStringSetList-class	XStringSetList-class
XStringViews	XStringViews-class
XStringViews-class	XStringViews-class
yeastSEQCHR1	yeastSEQCHR1
[,XStringPartialMatches-method	XStringPartialMatches-class
[[,ByPos_MIndex-method	MIndex-class
[[,PDict-method	PDict-class
[[,SparseList-method	Biostrings-internals
