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

 

   

Multiple Sequence Alignment

Bioconductor version: Release (3.4)

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")

 

PDF R Script msa - An R Package for Multiple Sequence Alignment
PDF   Reference Manual
Text   NEWS

Details

biocViews Alignment, MultipleComparison, MultipleSequenceAlignment, Sequencing, Software
Version 1.6.0
In Bioconductor since BioC 3.1 (R-3.2) (1.5 years)
License GPL (>= 2)
Depends R (>= 3.1.0), methods, Biostrings(>= 2.30.0)
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 odseq
Suggests Me
Build Report  

Package Archives

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

Package Source msa_1.6.0.tar.gz
Windows Binary msa_1.6.0.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) msa_1.6.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/msa/tree/release-3.4
Package Short Url http://bioconductor.org/packages/msa/
Package Downloads Report Download Stats

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