Package: msa
Type: Package
Title: Multiple Sequence Alignment
Version: 1.45.1
Date: 2026-06-08
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, MultipleAlignment, 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
Config/pak/sysreqs: make zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-06-08 10:11:39 UTC
RemoteUrl: https://github.com/bioc/msa
RemoteRef: HEAD
RemoteSha: 13ac2416f386805fc471243086b889276f64637d
Packaged: 2026-06-08 14:56:00 UTC; root
Author: Enrico Bonatesta [aut],
  Christoph Kainrath [aut],
  Ulrich Bodenhofer [aut, cre, ths]
Built: R 4.6.0; aarch64-apple-darwin23; 2026-06-08 15:06:42 UTC; unix
