msa: an R package for multiple sequence alignment | Zendy

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

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msa: an R package for multiple sequence alignment

Author(s) -

Ulrich Bodenhofer,

Enrico Bonatesta,

Christoph Horejš-Kainrath,

Sepp Hochreiter

Publication year - 2015

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btv494

Subject(s) - bioconductor , computer science , software , r package , sequence (biology) , multiple sequence alignment , interface (matter) , task (project management) , sequence alignment , software package , source code , data mining , programming language , operating system , biology , peptide sequence , engineering , biochemistry , genetics , bubble , maximum bubble pressure method , gene , systems engineering

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.

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