X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Fclustal.html;h=195171eecde4d5db845e10244dde9cadde2e2a67;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=dd436c8d94ed52e9158da14ce01ab388e698edbc;hpb=51b6a83c3eb462f1a0cb76a8b4111521a4554fac;p=jalview.git diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html index dd436c8..195171e 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
+ +
@@ -38,8 +58,8 @@ 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}
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}
+
- - + +