Dear Jalview team,
I would like to export my alignment as PNG from command line and I would like to have a png image with wrap sequence colour by identity percentage. Is it possible from command line options? How can I do that?
Thanks a lot,
Denise
Hi Denise,
The -props argument provides a way of styling the alignment.
First, make a backup of your current .jalview_properties (found in your home directory), and then adjust the default alignment formatting and colouring settings in the preferences dialog so your alignment is displayed as you’d like. Then make a backup of your adjusted .jalview_properties and pass it to jalview via the -props argument to apply the same styling during command line operation.
Let us know how you get on !
Jim.