Running Jalview from the command line

Jalview can be run from the command line, and provides a range of arguments.

There are a few different ways to do this:

Jalview's command line launch

Since version 2.11.2, the Jalview native application includes a launching shell script. This is the easiest way to launch an installed Jalview application from the command line.

To run the launch script, simply open a Terminal (or Command prompt on Windows), and type:


There are some important differences between the using the launching script and launching Jalview from its icon:

Adding the launch script to your path

If typing 'jalview' in the terminal prompt (or windows command line) doesn't work then you will need to add the location of the jalview launch script to your PATH.

How you do this depends on your operating system.

Older versions of Jalview

If you are using a version of Jalview prior to 2.11.2, you can still launch from the command line, but you will have to use a more platform specific way to launch and use command line arguments.

If you have installed Jalview via conda or another package manager then you most likely have a 'jalview' command available in your terminal shell's default path. Alternately, if you have built Jalview from source, then take a look at the doc/ file included in the source distribution.

Use '--help' to get more information on the command line arguments that Jalview accepts.

Passing JVM Arguments to Jalview
If you need to modify parameters for Jalview's Java Virtual Machine, or configure system properties, then take a look at the instructions for how to setting the JVM's maximum memory.

Changing Jalview's 'Look and Feel'
If you are experiencing issues with the font size or layout of Jalview's GUI, you can try changing Jalview's 'Look and feel' by specifying a custom system property 'laf' on startup (see setting the JVM's memory for instructions on how to do this for your platform).
For the Jalview standalone executable jar, simply provide one of the property settings before the -jar argument

The currently configured look and feel is logged to Jalview's console. Once the look and feel has been changed, it will be stored in Jalview's .jalview_properties file for future Jalview sessions. This property is PREFERRED_LAF and can also be used to set the Look and feel by editing your .jalview_properties file.