If you are running Jalview in Linux with a HiDPI or 4K monitor then the font size and menus are likely to be too small to be practical.

UPDATE: Jalview 2.11.1.1 and above should automatically detect a Linux HiDPI display, and scale the application appropriately if you are using the Java 11 version. You can download a newer installer from https://www.jalview.org/getdown/release/install4j/11/jalview-2_11_1_1-linux_x64-java_11.sh (coming soon!).

A previously installed version of the Java 11 version of Jalview should update automatically and will apply the HiDPI scaling the NEXT time it is launched after it auto-updates.

Please note that we have found a “drag-and-drop” positional error in the underlying Java components when using upscaling in Linux. This is detailed below.

ORIGINAL: To effectively remedy this, you will need a Java 11 version of Jalview. For Jalview 2.11.1.0 Java 11 is not officially supported but we are working towards that, so you can:

1. Download a Java 11 linux installer from https://www.jalview.org/getdown/release/install4j/11/jalview-2_11_1_0-linux_x64-java_11.sh
   (if you are using linux a platform other than intel 64 bit you will need to obtain a Java 11 JRE, e.g. from https://adoptopenjdk.net/, and then download the non-bundled-jre unix installer from [https://www.jalview.org/getdown/release/install4j/11/jalview-2_11_1_0-unix- java_11.sh](https://www.jalview.org/getdown/release/install4j/11/jalview- 2_11_1_0-unix-java_11.sh)).

2. Install as usual with the command

bash jalview-2_11_1_0-linux_x64-java_11.sh

3. Assuming this installed into the directory ~/opt/jalview, edit the file ~/opt/jalview/jalview and add onto the first blank line **export GDK_SCALE=2** so that the top of that file looks like

#!/bin/sh
export GDK_SCALE=2

# Uncomment the following line to override the JVM search sequence
# INSTALL4J_JAVA_HOME_OVERRIDE=
# Uncomment the following line to add additional VM parameters
# INSTALL4J_ADD_VM_PARAMS=
...

Jalview should now run at double sized resolution.

DRAG-AND-DROP ISSUE: When running Jalview (or any Java Swing application) with a scaling larger than 1 (most likely 2), the positional calculation when a drag-and-drop event occurs appears to be incorrect. This is most obvious when, for instance, dragging an alignment file from your file manager application onto Jalview when you have an existing alignment window open. If you drop the file over the existing alignment, the new file should be appended to the existing alignment. If you drop the file over Jalview but not over an existing alignment it should open in a new alignment window. Because the drop event’s position is miscalculated the results can be unexpected. See the issue JAL-3702 for more details.

For consistent behaviour, use the Jalview menu File→Input Alignment→From File to open a new alignment window. To append to an existing alignment window use that alignment window’s File→Add Sequences→From File option.