To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("msa")
In most cases, you don't need to download the package archive at all.
msa
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Multiple Sequence Alignment
Bioconductor version: Release (3.5)
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, Christoph Horejs-Kainrath, Ulrich Bodenhofer
Maintainer: Ulrich Bodenhofer <bodenhofer at bioinf.jku.at>
Citation (from within R,
enter citation("msa")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("msa")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("msa")
| R Script | msa - An R Package for Multiple Sequence Alignment | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Alignment, MultipleComparison, MultipleSequenceAlignment, Sequencing, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (2.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.1.0), methods, Biostrings(>= 2.40.0) |
| Imports | Rcpp (>= 0.11.1), BiocGenerics, IRanges(>= 1.20.0), S4Vectors, tools |
| LinkingTo | Rcpp |
| Suggests | Biobase, knitr, seqinr, ape, phangorn |
| SystemRequirements | GNU make |
| Enhances | |
| URL | http://www.bioinf.jku.at/software/msa/ |
| Depends On Me | |
| Imports Me | LymphoSeq, odseq |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | msa_1.8.0.tar.gz |
| Windows Binary | msa_1.8.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | msa_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/msa |
| Package Short Url | http://bioconductor.org/packages/msa/ |
| Package Downloads Report | Download Stats |
Documentation »
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