Running Jalview from the command line
Jalview can be run from the command line, and provides a range of arguments. These arguments can also be passed via .JVL files, which are opened automatically by the Jalview application when double-clicked in a file browser on Windows and OSX.The way that you launch Jalview from the command line depends on the platform you are on, and how it has been installed.
/PATH_TO_JALVIEW/Jalview -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal
\PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa
open /Applications/Jalview.app --args -open ~/myalignment.fa(put all the Jalview arguments after the --args parameter)
<Path to Java home>/bin/java -jar <Path to Jalview Jar>/jalview-all-1.8.jar -open myalignment.fa
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/building.md 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