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Bioconductor - msa (development version)

msa

This is the development version of msa; for the stable release version, see msa.

Multiple Sequence Alignment

Bioconductor version: Development (3.22)

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.

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

Maintainer: Ulrich Bodenhofer <ulrich at bodenhofer.com>

Citation (from within R, enter citation("msa")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("msa")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("msa")
msa - An R Package for Multiple Sequence Alignment PDF R Script Reference Manual PDF NEWS Text Details biocViews Alignment, MultipleComparison, MultipleSequenceAlignment, Sequencing, Software Version 1.41.0 In Bioconductor since BioC 3.1 (R-3.2) (10 years) License GPL (>= 2) Depends R (>= 3.3.0), methods, Biostrings(>= 2.40.0) Imports Rcpp (>= 0.11.1), BiocGenerics, IRanges(>= 1.20.0), S4Vectors, tools System Requirements GNU make URL https://github.com/UBod/msa See More Package Archives

Follow Installation instructions to use this package in your R session.

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