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 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,C,I,L,M,F,W,V	{>60%, WLVIMAFCYHP}
Hydrophobic	BLUE	C	{>60%, WLVIMAFCYHP}
Positive charge	RED	K,R	{>60%,KR},{>85%, K,R,Q}
Negative charge	MAGENTA	E	{>60%,KR},{>50%,QE},{>50%,ED},{>85%,E,Q,D}
Negative charge	MAGENTA	D	{>60%,KR}, {>85%, D,E,N}, {>50%,ED}
Polar	GREEN	N	{>50%, N}, {>85%, N,D}
		Q	{>60%,KR},{>50%,QE},{>85%,Q,T,K,R}
		S,T	{>60%, WLVIMAFCYHP}, {>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%, WLVIMAFCYHP}, {>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