SnapGene allows amino acid color highlighting based on three color schemes as detailed below.
Physicochemical Properties (Zappo)
Residues are coloured according to their physicochemical properties as follows:
Properties + Conservation (Clustal X)
Residues are colored according to their properties and conservation using the default Clustal X coloring scheme, as follows:
Transmembrane Tendency (Zhao and London)
Residues are coloured according to their "transmembrane tendency", as defined by Zhao and London, 2006: