Package: msa 1.45.1

Ulrich Bodenhofer

msa: Multiple Sequence Alignment

The 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.

Authors:Enrico Bonatesta [aut], Christoph Kainrath [aut], Ulrich Bodenhofer [aut, cre, ths]

msa_1.45.1.tar.gz
msa_1.45.1.zip(r-4.7)msa_1.45.1.zip(r-4.6)msa_1.45.1.zip(r-4.5)
msa_1.45.1.tgz(r-4.6-x86_64)msa_1.45.1.tgz(r-4.6-arm64)msa_1.45.1.tgz(r-4.5-x86_64)msa_1.45.1.tgz(r-4.5-arm64)
msa_1.45.1.tar.gz(r-4.7-arm64)msa_1.45.1.tar.gz(r-4.7-x86_64)msa_1.45.1.tar.gz(r-4.6-arm64)msa_1.45.1.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
msa/json (API)
NEWS

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

Bug tracker:https://github.com/ubod/msa/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:msa-1.45.0(bioc 3.24)msa-1.44.0(bioc 3.23)

multiplesequencealignmentalignmentmultiplecomparisonsequencingcpp

12.12 score 25 stars 8 packages 1.3k scripts 3.5k downloads 50 mentions 13 exports 10 dependencies

Last updated from:13ac2416f3. Checks:12 WARNING, 1 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING308
linux-devel-arm64WARNING324
linux-devel-x86_64WARNING351
source / vignettesOK516
linux-release-arm64WARNING326
linux-release-x86_64WARNING344
macos-release-arm64WARNING438
macos-release-x86_64WARNING942
macos-oldrel-arm64WARNING407
macos-oldrel-x86_64WARNING598
windows-develWARNING529
windows-releaseWARNING514
windows-oldrelWARNING528
wasm-releaseFAIL112

Exports:msamsaCheckNamesmsaClustalOmegamsaClustalWmsaConsensusSequencemsaConservationScoremsaConvertmsaMusclemsaPrettyPrintparamsprintshowversion

Dependencies:BiocGenericsBiostringscrayongenericsIRangesMultipleAlignmentRcppS4VectorsSeqinfoXVector

msa - An R Package for Multiple Sequence Alignment

Rendered frommsa.Rnwusingknitr::knitron Jun 08 2026.

Last update: 2024-04-25
Started: 2015-04-10

Readme and manuals

Help Manual

Help pageTopics
Multiple Sequence Alignmentmsa-package msaPackage
Unified interface to multiple sequence alignment algorithmsmsa
Check and fix sequence namesmsaCheckNames
Multiple Sequence Alignment with ClustalOmegamsaClustalOmega
Multiple Sequence Alignment with ClustalWmsaClustalW
Computation of Consensus Sequence from Multiple AlignmentmsaConsensusSequence msaConsensusSequence,matrix-method msaConsensusSequence,MultipleAlignment-method
Computation of Conservation Scores from Multiple AlignmentmsaConservationScore msaConservationScore,matrix-method msaConservationScore,MultipleAlignment-method
Convert Multiple Sequence Alignment for Other PackagesmsaConvert
Class 'MsaMetaData'class:MsaMetaData MsaMetaData MsaMetaData-class params,MsaMetaData-method version version,MsaMetaData-method
Classes 'MsaAAMultipleAlignment', 'MsaDNAMultipleAlignment', and 'MsaRNAMultipleAlignment'class:MsaAAMultipleAlignment class:MsaDNAMultipleAlignment class:MsaRNAMultipleAlignment MsaAAMultipleAlignment MsaAAMultipleAlignment-class MsaDNAMultipleAlignment MsaDNAMultipleAlignment-class MsaRNAMultipleAlignment MsaRNAMultipleAlignment-class params,MsaAAMultipleAlignment-method params,MsaDNAMultipleAlignment-method params,MsaRNAMultipleAlignment-method print,MsaAAMultipleAlignment-method print,MsaDNAMultipleAlignment-method print,MsaRNAMultipleAlignment-method show,MsaAAMultipleAlignment-method show,MsaDNAMultipleAlignment-method show,MsaRNAMultipleAlignment-method version,MsaAAMultipleAlignment-method version,MsaDNAMultipleAlignment-method version,MsaRNAMultipleAlignment-method
Multiple Sequence Alignment with MUSCLEmsaMuscle
Pretty-Printing of Multiple Sequence AlignmentsmsaPrettyPrint