Hello UGENE Team,
first, I want to thank you for this beautiful program, in the course of last 2 years it helped me a lot. One minor, in my opinion useful feature would be, if in MSA view one could color the columns manually, at will. This would allow to visualize, functional/structural properties of proteins at alignment level. In any case, thanks again a lot for your effort!!
Cheers,
Nikolai

Hello Dimitrii,
your second suggestion is interesting, but I meant rather the first one: a coloring scheme that does not color by bases/amino acids at all but lets you color the columns according to whatever you want to highlight.
Two variants of that idea would be: 1) if one could mark e.g. columns 4-16 and 45-66 and give them the class "alphahelix". Then mark columns 20-40 and classify them as "betasheet". And then say background of class "alphahelix" green, "betasheet" blue... Or variant 2), if one can just select columns 4-16 and make them green.
As I said, this could be used for highlighting either discrete properties of alignment regions - like structures, enzymatic centers and so on (here, variant 1 would be more convenient); or for gradient properties like selection strengths, with brighter colors corresponding to stronger selection (here, variant 2 is maybe more convenient). But generally, both goals work with both variants and I guess the use is quite versatile.
Cheers,
Nikolai