Package: msa
 Type: Package
 Title: Multiple Sequence Alignment

 Version: 1.20.1
 Date: 2020-09-01

 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>

 Description: 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.

 URL: http://www.bioinf.jku.at/software/msa/

 License: GPL (>= 2)
 Copyright: See file inst/COPYRIGHT

 Depends: R (>= 3.1.0), methods, Biostrings (>= 2.40.0)

 Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
         S4Vectors, tools

 Suggests: Biobase, knitr, seqinr, ape, phangorn

 LinkingTo: Rcpp

 SystemRequirements: GNU make

 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

         msaClustalOmega.R msaConvert.R msaCheckNames.R

 	msaConsensusSequence-methods.R msaConservationScore-methods.R

 biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
         Sequencing
 NeedsCompilation: yes