It is possible to apply different coloring schemes for an alignment, so that nucleotide or amino acid residues are colored depending on some rules.

To set another coloring scheme, select the required item in the main (Actions → Appearance → Colors) or context menu (Appearance → Colors) of the Alignment Editor, or in the Color combo box on the Highlighting tab on the Options Panel.

     <img width="500" src="/wiki/download/attachments/49447343/Coloring Schemes.png"/>

Note that the coloring schemes setting may interfere with other alignment highlighting settings (see e.g. Highlighting combo box on the Highlighting tab of the Options Panel). Thus, the colors may vary in this case from the described below.

Coloring Schemes for Nucleotides

The following schemes options are available for a nucleotide alignment:

Coloring Schemes for Amino Acids

The following schemes options are available for an amino acids alignment: