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-<head><title>Clustal Colour Scheme</title>
+<head>
+<title>Clustal Colour Scheme</title>
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td {
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-<p><em>Clustal X Colour Scheme</em></p>
- <p>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.</p>
- <p>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.</p>
-<div align="center">
- <p> </p><table border="1">
-<tr><th>Clustal X Default Colouring</th></tr>
- <tr>
- <td><table border="1">
-<tr><th>Residue at position</th><th>Applied Colour</th><th>{ Threshhold, Residue group }</th></tr>
-<tr><td>A,I,L,M,F,W,V</td><td bgcolor="#80a0f0">BLUE</td><td>{+60%, WLVIMAFCHP}</td></tr>
-<tr><td>R,K</td><td bgcolor="#f01505">RED</td><td>{+60%,KR},{+80%, K,R,Q}</td></tr>
-<tr><td>N</td><td bgcolor="#15c015">GREEN</td><td>{+50%, N}, {+85%, N,Y}</td></tr>
-<tr><td>C</td><td bgcolor="#80a0f0">BLUE</td>
-<td>{+60%, WLVIMAFCHP}</td></tr>
-<tr><td>C</td><td bgcolor="#f08080">PINK</td>
-<td>{100%, C}</td></tr>
-<tr><td>Q</td><td bgcolor="#15c015">GREEN</td><td>{+60%,KR},{+50%,QE},{+85%,Q,E,K,R}</td></tr>
-<tr><td>E</td><td bgcolor="#c048c0">MAGENTA</td><td>{+60%,KR},{+50%,QE},{+85%,E,Q,D}</td></tr>
-<tr><td>D</td><td bgcolor="#c048c0">MAGENTA</td><td>{+60%,KR}, {+85%, K,R,Q}, {+50%,ED}</td></tr>
-<tr><td>G</td><td bgcolor="#f09048">ORANGE</td><td>{+0%, G}</td></tr>
-<tr><td>H,Y</td><td bgcolor="#15a4a4">CYAN</td><td>{+60%, WLVIMAFCHP}, {+85%, W,Y,A,C,P,Q,F,H,I,L,M,V}</td></tr>
-<tr><td>P</td><td bgcolor="#c0c000">YELLOW</td><td>{+0%, P}</td></tr>
-<tr><td>S,T</td><td bgcolor="#15c015">GREEN</td><td>{+60%, WLVIMAFCHP}, {+50%, TS}, {+85%,S,T}</td></tr>
-</table>
-</td></tr></table>
-</div>
+ <p>
+ <strong>Clustal X Colour Scheme</strong>
+ </p>
+ <p>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.</p>
+ <p>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.
+ <br>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).</p>
+ <div align="center">
+ <p> </p>
+ <table border="1">
+ <tr>
+ <th>Clustal X Default Colouring</th>
+ </tr>
+ <tr>
+ <td><table border="1">
+ <tr>
+ <th>Category</th>
+ <th>Colour</th>
+ <th>Residue at position</th>
+ <th>{ Threshold, Residue group }</th>
+ </tr>
+ <tr>
+ <td rowspan="2">Hydrophobic</td>
+ <td rowspan="2" bgcolor="#80a0f0">BLUE</td>
+ <td>A,I,L,M,F,W,V</td>
+ <td>{>60%, WLVIMAFCHP}</td>
+ </tr>
+ <tr>
+ <td>C</td>
+ <td>{>60%, WLVIMAFCHP}</td>
+ </tr>
+ <tr>
+ <td>Positive charge</td>
+ <td bgcolor="#f01505">RED</td>
+ <td>K,R</td>
+ <td>{>60%,KR},{>80%, K,R,Q}</td>
+ </tr>
+ <tr>
+ <td rowspan="2">Negative charge</td>
+ <td rowspan="2" bgcolor="#c048c0">MAGENTA</td>
+ <td>E</td>
+ <td>{>60%,KR},{>50%,QE},{>85%,E,Q,D}</td>
+ </tr>
+ <tr>
+ <td>D</td>
+ <td>{>60%,KR}, {>85%, K,R,Q}, {>50%,ED}</td>
+ </tr>
+ <tr>
+ <td rowspan="3">Polar</td>
+ <td rowspan="3" bgcolor="#15c015">GREEN</td>
+ <td>N</td>
+ <td>{>50%, N}, {>85%, N,Y}</td>
+ </tr>
+ <tr>
+ <td>Q</td>
+ <td>{>60%,KR},{>50%,QE},{>85%,Q,E,K,R}</td>
+ </tr>
+ <tr>
+ <td>S,T</td>
+ <td>{>60%, WLVIMAFCHP}, {>50%, TS}, {>85%,S,T}</td>
+ </tr>
+ <tr>
+ <td>Cysteines</td>
+ <td bgcolor="#f08080">PINK</td>
+ <td>C</td>
+ <td>{>85%, C}</td>
+ </tr>
+ <tr>
+ <td>Glycines</td>
+ <td bgcolor="#f09048">ORANGE</td>
+ <td>G</td>
+ <td>{>0%, G}</td>
+ </tr>
+ <tr>
+ <td>Prolines</td>
+ <td bgcolor="#c0c000">YELLOW</td>
+ <td>P</td>
+ <td>{>0%, P}</td>
+ </tr>
+ <tr>
+ <td>Aromatic</td>
+ <td bgcolor="#15a4a4">CYAN</td>
+ <td>H,Y</td>
+ <td>{>60%, WLVIMAFCHP}, {>85%,
+ W,Y,A,C,P,Q,F,H,I,L,M,V}</td>
+ </tr>
+ <tr>
+ <td>Unconserved</td>
+ <td>WHITE</td>
+ <td>any / gap</td>
+ <td>If none of the above criteria are met</td>
+ </tr>
+ </table></td>
+ </tr>
+ </table>
+ </div>
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