The question is in the title: how one can highlight specific residues in the alignment/sequence in Geneious. Geneious can do it itself using several algorithms (agreements, disagreements etc.) but if one need to highlight something less specific, it can`t.

Eg, I have an alignment:

12345

aaaaa

aacaa

aaaaa

Geneious will automatically highlight "c" in the second row and/or all "a" in columns 1,2,4,5. While, I`m trying to figure out how to color (or to put it in box or whatever) any residue I want, eg, "a" in the 1st raw and 4 column.

If not in Geneious, probably, somebody knows an easy-to-use free software, (preferably for Win, but Ubuntu also ok) where I can do this?

thanks