It is possible to apply different coloring schemes for an alignment, so that nucleotide or amino acid characters residues are colored depending on some rules.
...
The following schemes options are available for an amino acids alignment:
- No colors — — do not color the characters background (i. e. white background is used for all characters).
- Buried index —
- Clustal X —
- Helix propensity —
- Hydrophobicity —
- Percentage Identity —
- Percentage Identity (gray) —
- Strand propensity —
- Tailor —
- Turn propensity —
- UGENE —
- Zappo — — amino acids residues are colored according to their physicochemical properties: alphatic/hydrophobic (characters ILVAM) - rose, aromatic (FWY) - orange, positive (KRH) - dark blue, negative (DE) - red, hydrophilic (STNQ) - light green, conformationally special (PG) - magenta, cysteine (C) - yellow.
- A custom scheme can be created and used with colors that depend on a character.
...