Perform pairwise sequence alignments

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Documentation for package ‘pwalign’ version 1.4.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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