Package: msa
Type: Package
Title: Multiple Sequence Alignment
Version: 1.0.0
Date: 2015-04-16
Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
Maintainer: Ulrich Bodenhofer <>
Description: This 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.
License: GPL (>= 2)
Copyright: See file inst/COPYRIGHT
Depends: R (>= 3.1.0), methods, Biostrings (>= 2.30.0)
Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors,
Suggests: Biobase, knitr
LinkingTo: Rcpp
VignetteBuilder: knitr
LazyLoad: yes
Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R 
         helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R
	 print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R 
biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison, Sequencing