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 }
--- | --- | ---
A,I,L,M,F,W,V | BLUE | {+60%, WLVIMAFCHP}
R,K | RED | {+60%,KR},{+80%, K,R,Q}
N | GREEN | {+50%, N}, {+85%, N,Y}
C | BLUE | {+60%, WLVIMAFCHP}
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}