Multiple Sequence Alignment for R Shiny

Visualises multiple sequence alignments dynamically within the Shiny web application framework.

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Basic Usage

msaR is a an htmlwidgets wrapper of the BioJS MSA viewer javascript library. msa will pass alignments to the BioJS MSA and has a convenience function that will handle the following formats:

  1. A character string which is interpreted to be a fasta file (opened by ape::read.dna)
  2. A DNAbin class object (ape)
  3. An XStringSet (Biostrings) including "DNAStringSet", "RNAStringSet", "AAStringSet", and "BStringSet"
  4. An XMultiple Alignment (Biostings) including "DNAMultipleAlignment","RNAMultipleAlignment", and"AAMultipleAlignment"

Any of these types of objects can be passed to msaR to create an html widget. This package in not on CRAN/Bioconductor and can be installed using devtools. See the online docs for an interactive version of this widget.

seqfile <- system.file("sequences","AHBA.aln", package="msaR")

All contributions are welcome! Please feel free to submit a pull request.

Support and Suggestions

If you have any problem or suggestion please open an issue here


This project is licensed under the Boost Software License 1.0.

If you use the MSAViewer on your website, it solely requires you to link to us




  • add nucleotide colro argument
  • Change the location of the image in the Readme file to be in man/figures as per CRAN policy.


  • Update msa.js to allow Overview Box to scale to the width of the parent Div.


  • Basic Release to CRAN

Reference manual

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0.3.0 by Zachary Charlop-Powers, 6 months ago

Browse source code at

Authors: Benedikt Rauscher [aut, cph], Zachary Charlop-Powers [cre, aut]

Documentation:   PDF Manual  

BSL-1.0 license

Imports ape, htmlwidgets

Suggests Biostrings, knitr, rmarkdown

See at CRAN