Viral Bioinformatics: Multiple sequence alignment – Jalview

This week€™s addition to the virology toolbox was written by Chris Upton

The Jalview package: a multiple alignment editor.

This software is primarily aimed at the alignment of protein sequences. Some of the key features are:

  • It allows you to edit the alignment
  • It has functions to display associated protein structures
  • It can connect to software to predict protein secondary structure
  • It€™s under active development
  • Jalview has great documentation and tutorials
  • More: Overview, Documentation


  1. Although you can install Jalview on your computer very easily, using the Start with Java Web Start button is even easier and ensures you always have the latest version of the software.
  2. There is also an Applet version of Jalview that is intended to be an alignment viewer €“ it doesn€™t have all the functionality.

If you use Jalview in your work, you should cite the Jalview 2 publication:

€¢ Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., Barton, G.J (2009), Jalview version 2: A Multiple Sequence Alignment and Analysis Workbench. Bioinformatics 25:1189-91.

€¢ Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor. Bioinformatics 20: 426-7.

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