MUSCLE manual
belvu alignment coloring
A given column has one color which indicates the average BLOSUM62 score of pairs of letters in the column: light blue >= 3, dark blue >= 1, light gray >= 0.2, no color otherwise. A letter is colored only if it has >= the average score against the rest of the column; this has the effect of coloring letters that are well-conserved but leaving letters that have low substitution scores uncolored in a given column.

This scheme is borrowed from Eric Sonnhammer's Belvu editor.

See source code colors.cpp, function AssignColorsCol().