Video Tip of The Week: Jalview for multiple sequence alignment editing and visualization

The multiple sequence alignment editing question recently on our What’s the Answer? feature was popular. We have covered MSA editors in the past, and we include a bit on Jalview in our Clustal tutorial, but I hadn’t revisited them lately. In preparation for that post I specifically looked over at the Jalview site, and I realized that they have recently provided a number of training videos to help people use their tools. So this week’s tip of the week will highlight them.

At the Jalview site, they give this brief description of the features:

Jalview is a free program for multiple sequence alignment editing, visualisation and analysis. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.

There are 2 flavors of Jalview. There is a JalviewLite applet you can demo by simply clicking on some examples at their site. Or you can run the Jalview desktop for more features (you can do this from the web or by downloading a local copy). The description on their About page will tell you more about the distinctions. You may also encounter Jalview that’s being incorporated in other tools. Here’s a handy list of those on their Community resources page.

On the Jalview online training Youtube channel, they have a number of videos. Some are general overview, some are specific tasks. For a general overview of what it does, this intro video will help you to decide if it’s a tool that would help you:

If you are ready to try it out, there are some handy tips in this video with more details about actually using the features of the software. It covers basic navigation, understanding the interface layout, working on editing, and good tips for accomplishing things efficiently.

For more of the philosophy and foundations of Jalview, check out their paper (linked below). And check out their other videos to go further.

Quick link:



Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
“Jalview Version 2 – a multiple sequence alignment editor and analysis workbench”
Bioinformatics25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp033

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