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- No colors — do not color the residues background (i. e. all residues have white background and black font).
- Buried index — depending on the frequency of occurrence inside a globule the amino acids residues are colored from light green (less frequent) to blue (most frequent).
- Clustal X — an emulation of the default color scheme in Clustal X, a graphical interface for the ClustalW multiple alignment program.
- Helix propensity — depending on helix propensity the residues are colored from magenta (the highest helix propensity) to green (the lowest one).
- Hydrophobicity — residues are colored based on their hydrophobicity. Most hydrophobic residues are red, most hydrophilic are blue.
- Percentage Identity — a residue background color depends on its presence in the column of the alignment: <=40% - white, 41-60% - light slate blue, 61-80% - medium slate blue, 81-100% dark slate blue.
- Percentage Identity (gray) — this coloring scheme is similar to Percentage Identity scheme, but shades of gray color are used instead of the slate blue color.
- Strand propensity — residues with highest strand propensity are yellow, with lowest are blue.
- Tailor — see this publication by William R.Taylor.
- Turn propensity — residues with highest turn propensity are red, with lowest are cyan.
- UGENE — this is the default coloring scheme, the following background colors are used for the residues: positive (KRH) - yellow, GPST - rose/red, FWY aromatic (FWY) - green, large alphatic hydrophobic (ILM) - blue, small hydrophobic (ST) - rose, GP - red, EX - gray.
- Zappo — amino acids residues are colored according to their physicochemical properties: alphatic/hydrophobic (residues 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.
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