msa
This is the development version of msa; for the stable release version, see msa.
Multiple Sequence Alignment
DOI: 10.18129/B9.bioc.msa
Bioconductor version: Development (3.24)
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, ths]
Maintainer: Ulrich Bodenhofer <ulrich at bodenhofer.com>
citation("msa")):Enrico Bonatesta, Christoph Kainrath, Ulrich Bodenhofer. msa: Multiple Sequence Alignment. doi:10.18129/B9.bioc.msa, R package version 1.45.6, https://bioconductor.org/packages/msa.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, MultipleComparison, MultipleSequenceAlignment, Sequencing, Software |
| Version | 1.45.6 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.3.0), methods, Biostrings (>= 2.40.0), MultipleAlignment |
| Imports | Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors, tools |
| System Requirements | GNU make |
| URL | https://github.com/UBod/msa |
See More
| Suggests | Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | ClustIRR, LymphoSeq, odseq, rhinotypeR, surfaltr |
| Suggests Me | AntibodyForests, bio3d, BOLDconnectR, idpr, SVAlignR |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | msa_1.45.6.tar.gz |
| Windows Binary (x86_64) | msa_1.45.6.zip |
| macOS Binary (big-sur-x86_64) | msa_1.45.6.tgz |
| macOS Binary (sonoma-arm64) | msa_1.45.6.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/msa |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/msa |
| Package Short Url | https://bioconductor.org/packages/msa/ |
| Package Downloads Report | Download Stats |