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 minimum percentage presence for any of the xx (or y) residue types.


Clustal X Default Colouring
Residue at position Applied Colour { Threshhold, Residue group }
R,K RED {+60%,KR},{+80%, K,R,Q}
N GREEN {+50%, N}, {+85%, N,Y}
C PINK {100%, C}
Q GREEN {+60%,KR},{+50%,QE},{+85%,Q,E,K,R}
E MAGENTA {+60%,KR},{+50%,QE},{+85%,E,Q,D}
D MAGENTA {+60%,KR}, {+85%, K,R,Q}, {+50%,ED}
G ORANGE {+0%, G}
H,Y CYAN {+60%, WLVIMAFCHP}, {+85%, W,Y,A,C,P,Q,F,H,I,L,M,V}
P YELLOW {+0%, P}
S,T GREEN {+60%, WLVIMAFCHP}, {+50%, TS}, {+85%,S,T}