Clustal X Colour Scheme

This is an emulation of the default colourscheme used for alignments in Clustal X, a graphical interface for the ClustalW multiple sequence alignment program. Each residue in the alignment is assigned a colour if the amino acid profile of the alignment at that position meets some minimum criteria specific for the residue type.

The table below gives these criteria as clauses: {>X%,xx,y}, where X is the threshold percentage presence for any of the xx (or y) residue types.
For example, K or R is coloured red if the column includes more than 60% K or R (combined), or more than 80% of either K or R or Q (individually).


Clustal X Default Colouring
Category Colour Residue at position { Threshold, Residue group }
Hydrophobic BLUE A,I,L,M,F,W,V {>60%, WLVIMAFCHP}
Positive charge RED K,R {>60%,KR},{>80%, K,R,Q}
Negative charge MAGENTA E {>60%,KR},{>50%,QE},{>85%,E,Q,D}
D {>60%,KR}, {>85%, K,R,Q}, {>50%,ED}
Polar GREEN N {>50%, N}, {>85%, N,Y}
Q {>60%,KR},{>50%,QE},{>85%,Q,E,K,R}
S,T {>60%, WLVIMAFCHP}, {>50%, TS}, {>85%,S,T}
Cysteines PINK C {>85%, C}
Glycines ORANGE G {>0%, G}
Prolines YELLOW P {>0%, P}
Aromatic CYAN H,Y {>60%, WLVIMAFCHP}, {>85%, W,Y,A,C,P,Q,F,H,I,L,M,V}
Unconserved WHITE any / gap If none of the above criteria are met