Clustal 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}