Annotation Colouring

Jalview allows the columns of an alignment to be coloured using any numerical annotation rows added to that alignment.

Select "Colour" "by Annotation..." to bring up the Colour by Annotation settings window.

You can also apply Colour by annotation for a particular annotation (or per-sequence set) by right-clicking an annotation row's label and selecting "Colour by Annotation..." or "Colour by Annotation (per Sequence)..." from the Annotation label popup menu. (Since Jalview 2.11.3)

The Colour by Annotation Settings Window