</div></td>
</tr>
- <tr>
- <td><div align="center">-annotations FILE</div></td>
- <td>Add precalculated annotations to the alignment. See <a href="annotationsFormat.html" target="NEW">Annotation
- File</a> description.</td>
- </tr>
- <tr>
- <td><div align="center">-fasta FILE</div></td>
+ <tr>
+ <td>
+ <div align="center">-annotations FILE</div>
+ </td>
+ <td>Add precalculated annotations to the alignment. See <a
+ href="annotationsFormat.html" target="NEW">Annotation File</a>
+ description.</td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"></div>
+ <td>
+ <div align="left"></div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-nodisplay</div>
+ <td>
+ <div align="left">Run Jalview without User Interface</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-props FILE</div>
+ <td>
+ <div align="left">Use the given Jalview properties file instead
+ of users default</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-tree FILE</div>
+ <td>
+ <div align="left">Load the given newick format tree file onto
+ the alignment</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-features FILE</div>
+ <td>
+ <div align="left">Use the given file to mark features on the
+ alignment</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-questionnaire URL</div>
+ <td>
+ <div align="left">Queries the given URL for information about
+ any Jalview user questionnaires</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-noquestionnaire</div>
+ <td>
+ <div align="left">Turn off questionnaire check</div>
+ </td>
+ </tr>
+ <tr><td>
+ <div align="center">-nousagestats</div>
+ <td>
+ <div align="left">Turn off google analytics usage tracking</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-dasserver nickname=URL</div>
+ <td>
+ <div align="left">Add and enable a <a href="dassettings.html">DAS server</a> with given
+ nickname (alphanumeric or underscores only) for retrieval of features
+ for all alignments<br>
+ Sources that also support the sequence command may be specified by prepending the URL with 'sequence:'<br>
+ <em>e.g.</em> sequence:http://localdas.somewhere.org/das/source</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-fetchfrom nickname</div>
+ <td>
+ <div align="left">Query a <a href="dassettings.html">DAS source</a> called nickname for features for the alignments
+ and display them</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-groovy FILE</div>
+ <td>
+ <div align="left">Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
+ arguments have been processed</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-fasta FILE</div>
+ </td>
- <td><div align="left">Create alignment file FILE in Fasta format.</div></td>
- </tr>
- <tr>
+ <td>
+ <div align="left">Create alignment file FILE in Fasta format.</div>
+ </td>
+ </tr>
+ <tr>
<td><div align="center">-clustal FILE</div></td>
<td><div align="left">Create alignment file FILE in Clustal format.</div></td>
</tr>
<td><div align="left">Create alignment file FILE in PIR format.</div></td>
</tr>
<tr>
+ <td><div align="center">-pfam FILE</div></td>
+ <td><div align="left">Create alignment file FILE in PFAM format.</div></td>
+ </tr>
+ <tr>
<td><div align="center">-blc FILE</div></td>
<td><div align="left">Create alignment file FILE in BLC format.</div></td>
</tr>