Package: msa
Type: Package
Title: Multiple Sequence Alignment
Version: 1.44.0
Date: 2025-11-11
Authors@R: c(person(given = "Enrico",
                    family = "Bonatesta",
		    role = c("aut")),
             person(given = "Christoph",
                    family = "Kainrath",
		    role = c("aut")),
             person(given = "Ulrich",
                    family = "Bodenhofer",
		    role = c("aut", "cre", "ths"),
		    email = "ulrich@bodenhofer.com"))
Maintainer: Ulrich Bodenhofer <ulrich@bodenhofer.com>
Description: 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.
URL: https://github.com/UBod/msa
License: GPL (>= 2)
Copyright: See file inst/COPYRIGHT
Depends: R (>= 3.3.0), methods, Biostrings (>= 2.40.0)
Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
        S4Vectors, tools
Suggests: Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign
LinkingTo: Rcpp
SystemRequirements: GNU make
VignetteBuilder: knitr
LazyLoad: yes
Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
        helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R
        print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R
        msaClustalOmega.R msaConvert.R msaCheckNames.R
        msaConsensusSequence-methods.R msaConservationScore-methods.R
biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
        Sequencing
NeedsCompilation: yes
git_url: https://git.bioconductor.org/packages/msa
git_branch: RELEASE_3_23
git_last_commit: ce990d6
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28
Packaged: 2026-04-28 22:56:38 UTC; biocbuild
Author: Enrico Bonatesta [aut],
  Christoph Kainrath [aut],
  Ulrich Bodenhofer [aut, cre, ths]
Built: R 4.6.0; aarch64-apple-darwin23; 2026-04-29 04:51:40 UTC; unix
