Msa: An R package for multiple sequence alignment

Ulrich Bodenhofer; Enrico Bonatesta; Christoph Horejš-Kainrath; Sepp Hochreiter

doi:10.1093/bioinformatics/btv494

Msa: An R package for multiple sequence alignment

Ulrich Bodenhofer, Enrico Bonatesta, Christoph Horejš-Kainrath, Sepp Hochreiter

Research output: Contribution to journal › Article › peer-review

377 Citations (Scopus)

Abstract

UNLABELLED: Although the R platform and the add-on packages of the Bioconductor project are widely used in bioinformatics, the standard task of multiple sequence alignment has been neglected so far. The msa package, for the first time, provides a unified R interface to the popular multiple sequence alignment algorithms ClustalW, ClustalOmega and MUSCLE. The package requires no additional software and runs on all major platforms. Moreover, the msa package provides an R interface to the powerful package shade which allows for flexible and customizable plotting of multiple sequence alignments.

AVAILABILITY AND IMPLEMENTATION: msa is available via the Bioconductor project: http://bioconductor.org/packages/release/bioc/html/msa.html. Further information and the R code of the example presented in this paper are available at http://www.bioinf.jku.at/software/msa/.

Original language	English
Pages (from-to)	3997-3999
Number of pages	3
Journal	Bioinformatics
Volume	31
Issue number	24
DOIs	https://doi.org/10.1093/bioinformatics/btv494
Publication status	Published - 3 Jul 2015
Externally published	Yes

Keywords

Algorithms
Animals
Sequence Alignment/methods
Software

Access to Document

10.1093/bioinformatics/btv494

Cite this

@article{4531f569cb1f4c23a47bfa4a2286ea80,

title = "Msa: An R package for multiple sequence alignment",

abstract = "UNLABELLED: Although the R platform and the add-on packages of the Bioconductor project are widely used in bioinformatics, the standard task of multiple sequence alignment has been neglected so far. The msa package, for the first time, provides a unified R interface to the popular multiple sequence alignment algorithms ClustalW, ClustalOmega and MUSCLE. The package requires no additional software and runs on all major platforms. Moreover, the msa package provides an R interface to the powerful package shade which allows for flexible and customizable plotting of multiple sequence alignments.AVAILABILITY AND IMPLEMENTATION: msa is available via the Bioconductor project: http://bioconductor.org/packages/release/bioc/html/msa.html. Further information and the R code of the example presented in this paper are available at http://www.bioinf.jku.at/software/msa/.",

keywords = "Algorithms, Animals, Sequence Alignment/methods, Software",

author = "Ulrich Bodenhofer and Enrico Bonatesta and Christoph Horej{\v s}-Kainrath and Sepp Hochreiter",

year = "2015",

month = jul,

day = "3",

doi = "10.1093/bioinformatics/btv494",

language = "English",

volume = "31",

pages = "3997--3999",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "24",

}

TY - JOUR

T1 - Msa

T2 - An R package for multiple sequence alignment

AU - Bodenhofer, Ulrich

AU - Bonatesta, Enrico

AU - Horejš-Kainrath, Christoph

AU - Hochreiter, Sepp

PY - 2015/7/3

Y1 - 2015/7/3

N2 - UNLABELLED: Although the R platform and the add-on packages of the Bioconductor project are widely used in bioinformatics, the standard task of multiple sequence alignment has been neglected so far. The msa package, for the first time, provides a unified R interface to the popular multiple sequence alignment algorithms ClustalW, ClustalOmega and MUSCLE. The package requires no additional software and runs on all major platforms. Moreover, the msa package provides an R interface to the powerful package shade which allows for flexible and customizable plotting of multiple sequence alignments.AVAILABILITY AND IMPLEMENTATION: msa is available via the Bioconductor project: http://bioconductor.org/packages/release/bioc/html/msa.html. Further information and the R code of the example presented in this paper are available at http://www.bioinf.jku.at/software/msa/.

AB - UNLABELLED: Although the R platform and the add-on packages of the Bioconductor project are widely used in bioinformatics, the standard task of multiple sequence alignment has been neglected so far. The msa package, for the first time, provides a unified R interface to the popular multiple sequence alignment algorithms ClustalW, ClustalOmega and MUSCLE. The package requires no additional software and runs on all major platforms. Moreover, the msa package provides an R interface to the powerful package shade which allows for flexible and customizable plotting of multiple sequence alignments.AVAILABILITY AND IMPLEMENTATION: msa is available via the Bioconductor project: http://bioconductor.org/packages/release/bioc/html/msa.html. Further information and the R code of the example presented in this paper are available at http://www.bioinf.jku.at/software/msa/.

KW - Algorithms

KW - Animals

KW - Sequence Alignment/methods

KW - Software

UR - http://www.scopus.com/inward/record.url?scp=84950284621&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btv494

DO - 10.1093/bioinformatics/btv494

M3 - Article

C2 - 26315911

AN - SCOPUS:84950284621

SN - 1367-4803

VL - 31

SP - 3997

EP - 3999

JO - Bioinformatics

JF - Bioinformatics

IS - 24

ER -

Msa: An R package for multiple sequence alignment

Abstract

Keywords

Access to Document

Other files and links

Fingerprint

Cite this