X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Fclustal.html;h=b3d44dbf1c49e3c5623d1b4b5fc0f309ed568396;hb=b1e2aea95b3839a1a53f809c579666075cd3d348;hp=488f7451f6714eb5196ddeeaaeb85f6ef344403a;hpb=6fa9683bef52d6709abb81840681e4fa452cafe7;p=jalview.git diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html index 488f745..b3d44db 100755 --- a/help/html/colourSchemes/clustal.html +++ b/help/html/colourSchemes/clustal.html @@ -1,52 +1,137 @@ - -
- - - - -Clustal X
-N | -G | -P | -B | -D | -
S | -C | -Y | -K | -X | -
Q | -W | -T | -R | -H | -
Z | -E | -A | -F | -M | -
L | -V | -I | -
+ 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 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 | +||||||||||||||||||||||||||||||||||||||||||||||||
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