msa

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

Multiple Sequence Alignment

Bioconductor version: Development (3.21)

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, MultipleComparison, MultipleSequenceAlignment, Sequencing, Software
Version	1.39.0
In Bioconductor since	BioC 3.1 (R-3.2) (9.5 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

Suggests	Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign
Linking To	Rcpp
Enhances
Depends On Me
Imports Me	LymphoSeq, odseq, surfaltr, SeedMatchR
Suggests Me	idpr, bio3d
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	msa_1.39.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/msa
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/msa
Bioc Package Browser	https://code.bioconductor.org/browse/msa/
Package Short Url	https://bioconductor.org/packages/msa/
Package Downloads Report	Download Stats