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

BBSRC Eastbio DTP PhD workshop

BBSRC Eastbio Doctoral Training Partnership PhD workshop for the students from St Andrews, Dundee, Edinburgh and Aberdeen University.

“Jalview – Dundee born and bred software to interactively visualise, analyse and present your multiple sequence alignments” by Dr Suzanne Duce & Dr Jim Procter at 11:00 – 12:00 

“Dataviz’ in 30 mins: Do’s, Don’ts, and where to learn more” by Dr Jim Proctor at 12:00 – 12:30

Jalview JS link

Fuzzy fonts in the alignment view on OSX Mojave (10.14.x)

On OSX Mojave, you may notice that sequences and IDs in the Jalview alignment window are hard to read. To fix this, first:

1. Save your work and shut down Jalview

2. Open a Terminal window (use spotlight or the Launcher and type 'Terminal' to locate the Terminal App), and type:


  defaults write -g CGFontRenderingFontSmoothingDisabled -bool NO

3. Start Jalview again and load an alignment to check that the fonts are now legible.

Jalview 2.10.5

Jalview 2.10.5 is a minor release that includes critical patches for users working with Ensembl, RNA secondary structure annotation, and those running Jalview on OSX with Java 10.


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