I don't know about those programs. I have used Mega but can't remember for sure. I think color code is a prefixed value that reflects the percentage of homology of any given amino acid across your query. It is arbitrary and for some programs you can assign yourself a color to a predefined percentage of homology. For example you can assign blue for 100%. So any amino acid that is colored blue means it is completely conserved and so on….

Sorry! What I meant is that you can calculate it yourself. Just count the number of colors and then divide it in equal intervals in term of percentage homology. If you have 10 colors then one color will correspond to [0-10] % homology, the second [10-20] %, etc….until you reach [90-100%]. Some programs may use just 4 colors. It is relatively easy to know what the interval of the percentage homology for each color. Just compute the total number of the same amino acid in a column that have the same color and divide it by the total. Hope that help.