Change the Analysis view color scheme

The foreground and background color schemes for the Analysis view are specified in the Analysis section of the Style panel. To open the section, click on the expand bar entitled Analysis, or choose View > Style > Analysis. Each available color scheme is described below:

Color Scheme	Description	Nucleotide Legend	Amino Acid Legend
Color by Chemistry	The default color scheme used by multiple DNASTAR applications. Amino acids are colored according to their side chain chemistry. While Color by Chemistry can be used for nucleotide sequences too, we recommend instead using a Solid background color for nucleotides and then selecting a Comparison like Color only non-conserved residues, Color only differences from reference, etc.
Physiochemical: Shapely	Matches the RasMol amino acid and RasMol nucleotide color schemes, which are, in turn, based on Robert Fletterick’s “Shapely models.”
Physiochemical: Zappo	Colors residues according to their physico-chemical properties, and is also used in JalView (Waterhouse et al., 2009).
Physiochemical: UGene	Unipro UGENE coloring scheme.
Spectral Colors: Taylor	Taken from Taylor (1997) and also used in JalView (Waterhouse et al., 2009).
Clustal X	Taken from Thompson et al. (1994). This color scheme is only available for protein alignments.	N/A
Grayscale – Percentage Identity	This option uses only black/white/gray and is suitable for publications requiring grayscale images.
Percentage Identity	This option uses only shades of slate blue.