Package: msa

Type: Package

Title: Multiple Sequence Alignment

Version: 1.43.1

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 = "[email protected]"))

Maintainer: Ulrich Bodenhofer <[email protected]>

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