Package: pwalign 1.9.1

Hervé Pagès

pwalign: Perform pairwise sequence alignments

The two main functions in the package are pairwiseAlignment() and stringDist(). The former solves (Needleman-Wunsch) global alignment, (Smith-Waterman) local alignment, and (ends-free) overlap alignment problems. The latter computes the Levenshtein edit distance or pairwise alignment score matrix for a set of strings.

Authors:Patrick Aboyoun [aut], Robert Gentleman [aut], Hervé Pagès [cre]

pwalign_1.9.1.tar.gz
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pwalign_1.9.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
pwalign/json (API)
NEWS

# Install 'pwalign' in R:
install.packages('pwalign', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bioconductor/pwalign/issues

Datasets:
  • BLOSUM100 - Predefined scoring matrices
  • BLOSUM45 - Predefined scoring matrices
  • BLOSUM50 - Predefined scoring matrices
  • BLOSUM62 - Predefined scoring matrices
  • BLOSUM80 - Predefined scoring matrices
  • PAM120 - Predefined scoring matrices
  • PAM250 - Predefined scoring matrices
  • PAM30 - Predefined scoring matrices
  • PAM40 - Predefined scoring matrices
  • PAM70 - Predefined scoring matrices
  • phiX174Phage - Versions of bacteriophage phiX174 complete genome and sample short reads
  • quPhiX174 - Versions of bacteriophage phiX174 complete genome and sample short reads
  • srPhiX174 - Versions of bacteriophage phiX174 complete genome and sample short reads
  • wtPhiX174 - Versions of bacteriophage phiX174 complete genome and sample short reads

On BioConductor:pwalign-1.9.1(bioc 3.24)pwalign-1.8.0(bioc 3.23)

alignmentsequencematchingsequencinggeneticsbioconductor-package

8.93 score 1 stars 111 packages 137 scripts 12k downloads 41 exports 8 dependencies

Last updated from:f1991c7341. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING156
linux-devel-arm64NOTE178
linux-devel-x86_64NOTE241
source / vignettesOK189
linux-release-arm64NOTE221
linux-release-x86_64NOTE233
macos-release-arm64NOTE154
macos-release-x86_64NOTE234
macos-oldrel-arm64NOTE155
macos-oldrel-x86_64NOTE221
windows-develNOTE158
windows-releaseNOTE201
windows-oldrelNOTE124
wasm-releaseOK103

Exports:alignedalignedPatternalignedSubjectas.matrixcompareStringsconsensusMatrixcoveragedeletionenderrorSubstitutionMatricesindelinsertionmismatchmismatchSummarymismatchTablencharneditnindelnmatchnmismatchnucleotideSubstitutionMatrixpairwiseAlignmentPairwiseAlignmentsPairwiseAlignmentsSingleSubjectparallel_slot_namesparallelVectorNamespatternpidqualitySubstitutionMatricesscoreshowstartstringDistsubjectsummarytoStringtypeunalignedViewswidthwritePairwiseAlignments

Dependencies:BiocGenericsBiostringscrayongenericsIRangesS4VectorsSeqinfoXVector

Pairwise Sequence Alignments

Rendered fromPairwiseAlignments.Rnwusingutils::Sweaveon Jun 07 2026.

Last update: 2024-03-21
Started: 2024-03-21

Readme and manuals

Help Manual

Help pageTopics
Utility functions related to sequence alignmentalign-utils compareStrings compareStrings,AlignedXStringSet0,AlignedXStringSet0-method compareStrings,character,character-method compareStrings,PairwiseAlignments,missing-method compareStrings,XString,XString-method compareStrings,XStringSet,XStringSet-method consensusMatrix,PairwiseAlignmentsSingleSubject-method coverage,AlignedXStringSet0-method coverage,PairwiseAlignmentsSingleSubject-method coverage,PairwiseAlignmentsSingleSubjectSummary-method mismatch,AlignedXStringSet0,missing-method mismatchSummary mismatchSummary,AlignedXStringSet0-method mismatchSummary,PairwiseAlignmentsSingleSubject-method mismatchSummary,PairwiseAlignmentsSingleSubjectSummary-method mismatchSummary,QualityAlignedXStringSet-method mismatchTable mismatchTable,AlignedXStringSet0-method mismatchTable,PairwiseAlignments-method mismatchTable,QualityAlignedXStringSet-method nedit nedit,PairwiseAlignments-method nedit,PairwiseAlignmentsSingleSubjectSummary-method nmatch,PairwiseAlignments,missing-method nmatch,PairwiseAlignmentsSingleSubjectSummary,missing-method nmismatch,AlignedXStringSet0,missing-method nmismatch,PairwiseAlignments,missing-method nmismatch,PairwiseAlignmentsSingleSubjectSummary,missing-method
AlignedXStringSet and QualityAlignedXStringSet objectsaligned aligned,AlignedXStringSet0-method AlignedXStringSet AlignedXStringSet-class AlignedXStringSet0 AlignedXStringSet0-class as.character,AlignedXStringSet0-method class:AlignedXStringSet class:AlignedXStringSet0 class:QualityAlignedXStringSet end,AlignedXStringSet0-method indel indel,AlignedXStringSet0-method nchar,AlignedXStringSet0-method nindel nindel,AlignedXStringSet0-method parallelVectorNames,AlignedXStringSet0-method parallel_slot_names,AlignedXStringSet0-method QualityAlignedXStringSet QualityAlignedXStringSet-class ranges,AlignedXStringSet0-method seqtype,AlignedXStringSet0-method show,AlignedXStringSet0-method start,AlignedXStringSet0-method toString,AlignedXStringSet0-method unaligned unaligned,AlignedXStringSet0-method width,AlignedXStringSet0-method
InDel objectsclass:InDel deletion deletion,InDel-method InDel InDel-class insertion insertion,InDel-method
Optimal Pairwise AlignmentpairwiseAlignment pairwiseAlignment,ANY,ANY-method pairwiseAlignment,ANY,QualityScaledXStringSet-method pairwiseAlignment,QualityScaledXStringSet,ANY-method pairwiseAlignment,QualityScaledXStringSet,QualityScaledXStringSet-method
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objectsaligned,PairwiseAlignmentsSingleSubject-method alignedPattern alignedPattern,PairwiseAlignments-method alignedSubject alignedSubject,PairwiseAlignments-method as.character,PairwiseAlignmentsSingleSubject-method as.matrix,PairwiseAlignmentsSingleSubject-method class:PairwiseAlignments class:PairwiseAlignmentsSingleSubject class:PairwiseAlignmentsSingleSubjectSummary deletion,PairwiseAlignments-method indel,PairwiseAlignments-method insertion,PairwiseAlignments-method length,PairwiseAlignmentsSingleSubjectSummary-method nchar,PairwiseAlignments-method nchar,PairwiseAlignmentsSingleSubjectSummary-method nindel,PairwiseAlignments-method nindel,PairwiseAlignmentsSingleSubjectSummary-method PairwiseAlignments PairwiseAlignments,character,character-method PairwiseAlignments,character,missing-method PairwiseAlignments,XString,XString-method PairwiseAlignments,XStringSet,missing-method PairwiseAlignments-class PairwiseAlignmentsSingleSubject PairwiseAlignmentsSingleSubject,character,character-method PairwiseAlignmentsSingleSubject,character,missing-method PairwiseAlignmentsSingleSubject,XString,XString-method PairwiseAlignmentsSingleSubject,XStringSet,missing-method PairwiseAlignmentsSingleSubject-class PairwiseAlignmentsSingleSubjectSummary PairwiseAlignmentsSingleSubjectSummary-class parallel_slot_names,PairwiseAlignments-method pattern pattern,PairwiseAlignments-method score,PairwiseAlignments-method score,PairwiseAlignmentsSingleSubjectSummary-method seqtype,PairwiseAlignments-method show,PairwiseAlignments-method show,PairwiseAlignmentsSingleSubjectSummary-method subject,PairwiseAlignments-method summary,PairwiseAlignmentsSingleSubject-method toString,PairwiseAlignmentsSingleSubject-method type type,PairwiseAlignments-method type,PairwiseAlignmentsSingleSubjectSummary-method Views,PairwiseAlignmentsSingleSubject-method
Write a PairwiseAlignments object to a filePairwiseAlignments-io writePairwiseAlignments
Versions of bacteriophage phiX174 complete genome and sample short readsphiX174Phage quPhiX174 srPhiX174 wtPhiX174
Percent Sequence Identitypid pid,PairwiseAlignments-method
Predefined scoring matricesBLOSUM100 BLOSUM45 BLOSUM50 BLOSUM62 BLOSUM80 PAM120 PAM250 PAM30 PAM40 PAM70 predefined_scoring_matrices
String Distance/Alignment Score MatrixstringDist stringDist,character-method stringDist,QualityScaledXStringSet-method stringDist,XStringSet-method
Utilities to generate substitution matriceserrorSubstitutionMatrices nucleotideSubstitutionMatrix qualitySubstitutionMatrices substitution_matrices