<td>jnetfile</td>
<td>fileName</td>
<td>Secondary structure predictions from a <a
- href="http://www.compbio.dundee.ac.uk/~www-jpred/">Jnet</a> Concise
- file will be added to the first sequence in the alignment.</td>
+ href="http://www.compbio.dundee.ac.uk/~www-jpred/">JPred</a> Concise
+ file will be added to the first sequence in the alignment.<br/>
+ <em>jpredfile</em> can be used interchangeably with this parameter.</td>
</tr>
<tr>
<td>PDBfile(x)</td>
<td>defaultColour</td>
<td> <em>One of: </em><br>
Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix
- Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, T-Coffee Scores, RNA Helices</td>
+ Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, T-Coffee Scores, RNA Helices</td>
<td>Default is no colour.</td>
</tr>
<tr>
<td>Default is true.</td>
</tr>
<tr>
+ <td>showOccupancy</td>
+ <td>true <em>or</em> false</td>
+ <td>Default is true.</td>
+ </tr>
+ <tr>
<td>sortBy</td>
<td> Id <em>, </em> Pairwise Identity<em>, or</em> Length</td>
<td> Sorts the alignment on startup</td>