# Perform pairwise sequence alignments

## Documentation for package ‘pwalign’ version 1.8.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E I L M N P Q R S T U V W

## -- A --

align-utils | Utility functions related to sequence alignment
aligned | AlignedXStringSet and QualityAlignedXStringSet objects
aligned-method | AlignedXStringSet and QualityAlignedXStringSet objects
aligned-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
alignedPattern | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
alignedPattern-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
alignedSubject | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
alignedSubject-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
AlignedXStringSet | AlignedXStringSet and QualityAlignedXStringSet objects
AlignedXStringSet-class | AlignedXStringSet and QualityAlignedXStringSet objects
AlignedXStringSet0 | AlignedXStringSet and QualityAlignedXStringSet objects
AlignedXStringSet0-class | AlignedXStringSet and QualityAlignedXStringSet objects
as.character-method | AlignedXStringSet and QualityAlignedXStringSet objects
as.character-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
as.matrix-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects

## -- B --

BLOSUM100 | Predefined scoring matrices
BLOSUM45 | Predefined scoring matrices
BLOSUM50 | Predefined scoring matrices
BLOSUM62 | Predefined scoring matrices
BLOSUM80 | Predefined scoring matrices

## -- C --

class:AlignedXStringSet | AlignedXStringSet and QualityAlignedXStringSet objects
class:AlignedXStringSet0 | AlignedXStringSet and QualityAlignedXStringSet objects
class:InDel | InDel objects
class:PairwiseAlignments | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
class:PairwiseAlignmentsSingleSubject | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
class:PairwiseAlignmentsSingleSubjectSummary | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
class:QualityAlignedXStringSet | AlignedXStringSet and QualityAlignedXStringSet objects
compareStrings | Utility functions related to sequence alignment
compareStrings-method | Utility functions related to sequence alignment
consensusMatrix-method | Utility functions related to sequence alignment
coverage-method | Utility functions related to sequence alignment

## -- D --

deletion | InDel objects
deletion-method | InDel objects
deletion-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects

## -- E --

end-method | AlignedXStringSet and QualityAlignedXStringSet objects
errorSubstitutionMatrices | Utilities to generate substitution matrices

## -- I --

InDel | InDel objects
indel | AlignedXStringSet and QualityAlignedXStringSet objects
InDel-class | InDel objects
indel-method | AlignedXStringSet and QualityAlignedXStringSet objects
indel-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
insertion | InDel objects
insertion-method | InDel objects
insertion-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects

## -- L --

length-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects

## -- M --

mismatch-method | Utility functions related to sequence alignment
mismatchSummary | Utility functions related to sequence alignment
mismatchSummary-method | Utility functions related to sequence alignment
mismatchTable | Utility functions related to sequence alignment
mismatchTable-method | Utility functions related to sequence alignment

## -- N --

nchar-method | AlignedXStringSet and QualityAlignedXStringSet objects
nchar-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
nedit | Utility functions related to sequence alignment
nedit-method | Utility functions related to sequence alignment
nindel | AlignedXStringSet and QualityAlignedXStringSet objects
nindel-method | AlignedXStringSet and QualityAlignedXStringSet objects
nindel-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
nmatch-method | Utility functions related to sequence alignment
nmismatch-method | Utility functions related to sequence alignment
nucleotideSubstitutionMatrix | Utilities to generate substitution matrices

## -- P --

pairwiseAlignment | Optimal Pairwise Alignment
pairwiseAlignment-method | Optimal Pairwise Alignment
PairwiseAlignments | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignments-class | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignments-io | Write a PairwiseAlignments object to a file
PairwiseAlignments-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignmentsSingleSubject | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignmentsSingleSubject-class | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignmentsSingleSubject-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignmentsSingleSubjectSummary | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignmentsSingleSubjectSummary-class | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PAM120 | Predefined scoring matrices
PAM250 | Predefined scoring matrices
PAM30 | Predefined scoring matrices
PAM40 | Predefined scoring matrices
PAM70 | Predefined scoring matrices
parallelVectorNames-method | AlignedXStringSet and QualityAlignedXStringSet objects
parallel_slot_names-method | AlignedXStringSet and QualityAlignedXStringSet objects
parallel_slot_names-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
pattern | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
pattern-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
phiX174Phage | Versions of bacteriophage phiX174 complete genome and sample short reads
pid | Percent Sequence Identity
pid-method | Percent Sequence Identity
predefined_scoring_matrices | Predefined scoring matrices

## -- Q --

QualityAlignedXStringSet | AlignedXStringSet and QualityAlignedXStringSet objects
QualityAlignedXStringSet-class | AlignedXStringSet and QualityAlignedXStringSet objects
qualitySubstitutionMatrices | Utilities to generate substitution matrices
quPhiX174 | Versions of bacteriophage phiX174 complete genome and sample short reads

## -- R --

ranges-method | AlignedXStringSet and QualityAlignedXStringSet objects

## -- S --

score-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
seqtype-method | AlignedXStringSet and QualityAlignedXStringSet objects
seqtype-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
show-method | AlignedXStringSet and QualityAlignedXStringSet objects
show-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
srPhiX174 | Versions of bacteriophage phiX174 complete genome and sample short reads
start-method | AlignedXStringSet and QualityAlignedXStringSet objects
stringDist | String Distance/Alignment Score Matrix
stringDist-method | String Distance/Alignment Score Matrix
subject-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
substitution_matrices | Utilities to generate substitution matrices
summary-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects

## -- T --

toString-method | AlignedXStringSet and QualityAlignedXStringSet objects
toString-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
type | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
type-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects

## -- U --

unaligned | AlignedXStringSet and QualityAlignedXStringSet objects
unaligned-method | AlignedXStringSet and QualityAlignedXStringSet objects

## -- V --

Views-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects

## -- W --

width-method | AlignedXStringSet and QualityAlignedXStringSet objects
writePairwiseAlignments | Write a PairwiseAlignments object to a file
wtPhiX174 | Versions of bacteriophage phiX174 complete genome and sample short reads