Tips on installing Jalview on the Microsoft Surface Pro 3 (Windows 8.1)

I just got a Surface Pro 3 tablet and so naturally wanted to install Jalview on it. This is pretty straightforward, but could be confusing or offputting for some potential users, so thought I would post the list. We'll also put this in a FAQ on the website in due course.

1. If you do the Java webstart option the machine says it does not know what to do with the .jnlp file, so sends you to the App store to find an app that can open it. Unfortunately, the "app" it needs (Java) is not in the App store, so you get nowhere.

2. What you have to do is go to and install Java first from there. This should go fairly smoothly (it did for me).

3. Once you have Java installed, then click on the Jalview webstart option again from the Jalview home page. For me, Jalview did not start up the first time I tried this, but it worked perfectly after I quit and tried again.

Jalview is not yet muti-touch-aware, so drag, pinch to zoom etc don't work. Cascading menus also always cascade to the right regardless of the settings you make on the tablet for right or left-handed use, so you need to select menus with your left hand, or use the stylus left-handed.

We plan to make Jalview fully compatible with tablets and touch in a future release.

Happy Jalviewing!



Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology
College of Life Sciences | University of Dundee, Scotland, UK |
Tel: +44 1382 385860 | | twitter: @gjbarton
The University of Dundee is registered Scottish charity: No.SC015096