I have been using Jalview 188.8.131.52 to prepare sequence alignment for publications. One feature that will be very helpful is: do not include gaps while showing the scale above. Is it doable with current version? Many thank for your help!
The ruler can be numbered according to position of one of the sequences if you open the sequence ID, and from that sequence ID’s submenu select ‘Mark as reference’.
See the help docs https://www.jalview.org/help/html/calculations/referenceseq.html
Thank you very much for your help! It is VERY helpful to me!