Looking for the 'Launch Jalview' buttons ?

You need to download an installer to run Jalview 2.11.
You can still use webstart to access old versions of Jalview in the version archive

How do I set web proxy settings for Jalview's auto-updater and web services?


Jalview uses a launcher (called getdown, see https://github.com/threerings/getdown) that runs an auto-updater for Jalview and verifies Jalview files by checking the Jalview web site.  Whilst the launcher checks for existing system proxy settings, sometimes it does not find those settings.  In this case it may pop up a window asking for proxy settings.  If this does not happen, and proxy settings are required, you can create a file called

Jalview 2.11.0

Jalview 2.11.0 introduces support for loading VCF files, and new filters and shading models for sequence features. Under the hood, we've addressed many bugs, and also made some important changes in the way the Jalview desktop is installed and launched.

Jalview has encountered an error during launch

If you've been redirected to this FAQ then it probably means that the Jalview Native application has encountered an error whilst trying to start. Here are some tips for various problems:

Problems on Windows:

If your installation of Jalview goes fine, but double clicking on the Jalview icon does not produce any error message, window or any other activity (other than the spinning blue circle) this might be caused by a space character in Jalview's installation folder.  To fix this:

Jalview's menus and fonts are too small on my Windows machine !

When Jalview is run on WIndows machines with high resolution displays (e.g. 4K, retina, etc) resolution screens, you might find that all the menus, window titles, and alignment data are really tiny. That's because on high-resolution displays, all the windows and fonts have to be magnified so that you can read them, and the fix is to ask Windows to do the same for the Jalview application.

Instructions on how to do this can be found in several places on the 'net. Your milage may vary so please let us know if you are having problems via the jalview-discuss AT jalview.org mailing list !

See https://pivotce.com/2017/12/11/fix-java-applications-for-high-dpi-display/ for the following solution which should work for launching Jalview via webstart on machines with Java 8 installed.

  1. Close Jalview
  2. Find java.exe and/or javaw.exe likely found in C:\Program Files\Java\jre(version#)\bin.
  3. Right click on it and select -> Properties
  4. Go to Compatibility tab
  5. Check Override high DPI scaling behavior.
  6. Choose System for Scaling performed by:
  7. Click OK
  8. Relaunch Jalview


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