The letterconf command can generate a features file for the popular Jalview alignment viewer and editor.
In Jalview, first load the alignment then load annotations as shown in the screenshot below.
The feature file format is documented here: http://www.jalview.org/help/html/features/featuresFormat.html
The first ten lines of the feature file specify the colors for letter confidence values 0 through 9. Colors are specified as 6-digit hex values RRGGBB, as shown below. You can change the colors by editing this file.
LC0 A00000
LC1 902020
LC2 803030
LC3 703030
LC4 603030
LC5 404040
LC6 407040
LC7 308030
LC8 009000
LC9 00A000
STARTGROUP Muscle5_LetterConfs
- 1o20_A 0 1 54 LC9
- 1o20_A 0 55 55 LC6
