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
as.character,AlignedXStringSet0-method	AlignedXStringSet-class
as.character,PairwiseAlignmentsSingleSubject-method	PairwiseAlignments-class
as.matrix,PairwiseAlignmentsSingleSubject-method	PairwiseAlignments-class
BLOSUM100	predefined_scoring_matrices
BLOSUM45	predefined_scoring_matrices
BLOSUM50	predefined_scoring_matrices
BLOSUM62	predefined_scoring_matrices
BLOSUM80	predefined_scoring_matrices
class:AlignedXStringSet	AlignedXStringSet-class
class:AlignedXStringSet0	AlignedXStringSet-class
class:InDel	InDel-class
class:PairwiseAlignments	PairwiseAlignments-class
class:PairwiseAlignmentsSingleSubject	PairwiseAlignments-class
class:PairwiseAlignmentsSingleSubjectSummary	PairwiseAlignments-class
class:QualityAlignedXStringSet	AlignedXStringSet-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
consensusMatrix,PairwiseAlignmentsSingleSubject-method	align-utils
coverage,AlignedXStringSet0-method	align-utils
coverage,PairwiseAlignmentsSingleSubject-method	align-utils
coverage,PairwiseAlignmentsSingleSubjectSummary-method	align-utils
deletion	InDel-class
deletion,InDel-method	InDel-class
deletion,PairwiseAlignments-method	PairwiseAlignments-class
end,AlignedXStringSet0-method	AlignedXStringSet-class
errorSubstitutionMatrices	substitution_matrices
InDel	InDel-class
indel	AlignedXStringSet-class
indel,AlignedXStringSet0-method	AlignedXStringSet-class
indel,PairwiseAlignments-method	PairwiseAlignments-class
InDel-class	InDel-class
insertion	InDel-class
insertion,InDel-method	InDel-class
insertion,PairwiseAlignments-method	PairwiseAlignments-class
length,PairwiseAlignmentsSingleSubjectSummary-method	PairwiseAlignments-class
mismatch,AlignedXStringSet0,missing-method	align-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
nchar,AlignedXStringSet0-method	AlignedXStringSet-class
nchar,PairwiseAlignments-method	PairwiseAlignments-class
nchar,PairwiseAlignmentsSingleSubjectSummary-method	PairwiseAlignments-class
nedit	align-utils
nedit,PairwiseAlignments-method	align-utils
nedit,PairwiseAlignmentsSingleSubjectSummary-method	align-utils
nindel	AlignedXStringSet-class
nindel,AlignedXStringSet0-method	AlignedXStringSet-class
nindel,PairwiseAlignments-method	PairwiseAlignments-class
nindel,PairwiseAlignmentsSingleSubjectSummary-method	PairwiseAlignments-class
nmatch,PairwiseAlignments,missing-method	align-utils
nmatch,PairwiseAlignmentsSingleSubjectSummary,missing-method	align-utils
nmismatch,AlignedXStringSet0,missing-method	align-utils
nmismatch,PairwiseAlignments,missing-method	align-utils
nmismatch,PairwiseAlignmentsSingleSubjectSummary,missing-method	align-utils
nucleotideSubstitutionMatrix	substitution_matrices
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
PAM120	predefined_scoring_matrices
PAM250	predefined_scoring_matrices
PAM30	predefined_scoring_matrices
PAM40	predefined_scoring_matrices
PAM70	predefined_scoring_matrices
parallelVectorNames,AlignedXStringSet0-method	AlignedXStringSet-class
parallel_slot_names,AlignedXStringSet0-method	AlignedXStringSet-class
parallel_slot_names,PairwiseAlignments-method	PairwiseAlignments-class
pattern,PairwiseAlignments-method	PairwiseAlignments-class
phiX174Phage	phiX174Phage
pid	pid
pid,PairwiseAlignments-method	pid
predefined_scoring_matrices	predefined_scoring_matrices
QualityAlignedXStringSet	AlignedXStringSet-class
QualityAlignedXStringSet-class	AlignedXStringSet-class
qualitySubstitutionMatrices	substitution_matrices
quPhiX174	phiX174Phage
ranges,AlignedXStringSet0-method	AlignedXStringSet-class
score,PairwiseAlignments-method	PairwiseAlignments-class
score,PairwiseAlignmentsSingleSubjectSummary-method	PairwiseAlignments-class
seqtype,AlignedXStringSet0-method	AlignedXStringSet-class
seqtype,PairwiseAlignments-method	PairwiseAlignments-class
show,AlignedXStringSet0-method	AlignedXStringSet-class
show,PairwiseAlignments-method	PairwiseAlignments-class
show,PairwiseAlignmentsSingleSubjectSummary-method	PairwiseAlignments-class
srPhiX174	phiX174Phage
start,AlignedXStringSet0-method	AlignedXStringSet-class
stringDist	stringDist
stringDist,character-method	stringDist
stringDist,QualityScaledXStringSet-method	stringDist
stringDist,XStringSet-method	stringDist
subject,PairwiseAlignments-method	PairwiseAlignments-class
substitution_matrices	substitution_matrices
summary,PairwiseAlignmentsSingleSubject-method	PairwiseAlignments-class
toString,AlignedXStringSet0-method	AlignedXStringSet-class
toString,PairwiseAlignmentsSingleSubject-method	PairwiseAlignments-class
type	PairwiseAlignments-class
type,PairwiseAlignments-method	PairwiseAlignments-class
type,PairwiseAlignmentsSingleSubjectSummary-method	PairwiseAlignments-class
unaligned	AlignedXStringSet-class
unaligned,AlignedXStringSet0-method	AlignedXStringSet-class
Views,PairwiseAlignmentsSingleSubject-method	PairwiseAlignments-class
width,AlignedXStringSet0-method	AlignedXStringSet-class
writePairwiseAlignments	PairwiseAlignments-io
wtPhiX174	phiX174Phage
