First noticed by Julien Roux:
> I am trying to create a jalview file (.jar) including an amino-acid alignment, the associated tree and some annotations.
> To do this, I want to use the command line. I tried:
java -Djava.ext.dirs=/Applications/Jalview/lib -cp /Applications/Jalview/Jalview.jar jalview.bin.Jalview -open my_aln.fas -colour ZAPPO -annotations my_annot.jalview -tree my_tree.nwk -jalview test.jar
> This works fine and creates the test.jar file correctly. However, when I add the -nodisplay option to do this without User Interface,
> the file test.jar does not include the associated tree. Is this a bug or I am doing something wrong?