For the covariation color scheme, I want to generate random colors so I don't have to worry about storing an index of colors for an unknown number of helices. I found a nice algorithm at stackoverflow.com. I set up everything for the covariation color scheme and tried out the random color selection for each nucleotide.
Examples are below. I like the first example that uses pastels, but I worry that the colors are not distinct enough from each other. The problem with the second example is that the dark colors make it impossible to read the nucleotide; I could figure out how to make the text white in those cases.