Note these color schemes are only available for multiple alignment of protein sequences (3 or more protein sequences). These color schemes are not available for pairwise protein alignments.
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: