X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Fclustal.html;h=33455dca07a690b9cfe52e1a475cc8490c173f93;hb=b4b901505310c3bdd1809f122abed6799c2fa664;hp=7241e32aca12a95bdd1ec428a6384cb06a21d9c7;hpb=8fef38d29a5832b91f545e3cba7da74cb9aef501;p=jalview.git diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html index 7241e32..33455dc 100755 --- a/help/html/colourSchemes/clustal.html +++ b/help/html/colourSchemes/clustal.html @@ -1,28 +1,48 @@ - -Clustal Colour Scheme - - - - -

Clustal X Colour Scheme

+ + +Clustal Colour Scheme + + + + +

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 + 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.

-
-

 

+ where X is the minimum percentage presence for any of the xx (or y) residue types.

+
+

 

- -
Clustal X Default Colouring
+ +
@@ -35,11 +55,11 @@ td { - + -
Residue at positionApplied Colour{ Threshhold, Residue group }
A,I,L,M,F,W,VBLUE{+60%, WLVIMAFCHP}
R,KRED{+60%,KR},{+80%, K,R,Q}
EMAGENTA{+60%,KR},{+50%,QE},{+85%,E,Q,D}
DMAGENTA{+60%,KR}, {+85%, K,R,Q}, {+50%,ED}
GORANGE{+0%, G}
H,YCYAN{+60%, WLVIMAFCHP}, {+85%, W,Y,A,C,P,Q,F,H,I,L,M,V}
H,YCYAN{+60%, WLVIMAFCHP}, {+85%, W,Y,A,C,P,Q,F,H,I,L,M,V}
PYELLOW{+0%, P}
S,TGREEN{+60%, WLVIMAFCHP}, {+50%, TS}, {+85%,S,T}
+
- - + +