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 http://www.jalview.org/examples/jpred_msa.fasta -annotations http://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, then take a
look at the instructions for how to setting
the JVM's maximum memory.