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+<title>Summary of Command Line Arguments (version 2.11.3.0 onwards)</title>
+<body>
+
+ <h1>Summary of Command Line Arguments (version 2.11.3.0 onwards)</h1>
+
+ <p>
+ See <a href="clarguments-ng.html">Jalview Command Line Arguments (next generation)</a>
+ for more explanation about using Jalview's command line arguments.
+ </p>
+
+ <table border="1" cellpadding="3">
+ <tr>
+ <td><strong>argument</strong></td>
+ <td><strong>action</strong></td>
+ <td><strong>subval modifiers</strong> (optional)</td>
+ <td align="center"><strong>linked</strong> (optional)</td>
+ </tr>
+
+ <tr>
+ <td><code>--open <em>filename/URL ...</em></code></td>
+ <td>
+ Opens one or more alignment files in new alignment windows.
+ <a href="clarguments-ng.html#open">Examples</a>.
+ </td>
+ <td>
+ <code>
+ colour=<em>colourscheme</em>,
+ title=<em>title</em>,
+ features=<em>featurefile</em>,
+ annotations=<em>annotationfile</em>,
+ tree=<em>treefile</em>,
+ showannotations,
+ ssannotations,
+ sortbytree,
+ wrap
+ </code>
+ </td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr>
+ <td><code>--append <em>filename/URL ...</em></code></td>
+ <td>Appends one or more alignment files to an open alignment window (or opens a new alignment if none already open).</td>
+ <td>
+ <code>
+ colour=<em>colourscheme</em>,
+ title=<em>title</em>,
+ features=<em>featurefile</em>,
+ annotations=<em>annotationfile</em>,
+ tree=<em>treefile</em>,
+ showannotations,
+ ssannotations,
+ sortbytree,
+ wrap
+ </code>.
+ <a href="clarguments-ng.html#append">Examples</a>.
+ </td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr>
+ <td><code>--title <em>"title"</em></code></td>
+ <td>Specifies the title for the open alignment window.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr>
+ <td><code>--colour <em>colourscheme</em></code></td>
+ <td>Applies the given colour scheme to the open alignment window. Valid values are:
+ <code>clustal</code>,
+ <code>blosum62</code>,
+ <code>pc-identity</code>,
+ <code>zappo</code>,
+ <code>taylor</code>,
+ <code>gecos-flower</code>,
+ <code>gecos-blossom</code>,
+ <code>gecos-sunset</code>,
+ <code>gecos-ocean</code>,
+ <code>hydrophobic</code>,
+ <code>helix-propensity</code>,
+ <code>strand-propensity</code>,
+ <code>turn-propensity</code>,
+ <code>buried-index</code>,
+ <code>nucleotide</code>,
+ <code>nucleotide-ambiguity</code>,
+ <code>purine-pyrimidine</code>,
+ <code>rna-helices</code>,
+ <code>t-coffee-scores</code>,
+ <code>sequence-id</code>.
+ <a href="clarguments-ng.html#colour">Examples</a>.
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr>
+ <td><code>--features <em>filename/URL</em></code></td>
+ <td>Add a feature file to the open alignment.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+
+ <tr>
+ <td><code>--tree <em>filename/URL</em></code></td>
+ <td>Add a tree file to the open alignment.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr>
+ <td><code>--sortbytree / --nosortbytree</code></td>
+ <td>Enforces sorting (or not sorting) the alignment in the order of an attached phylogenetic tree.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>--annotations <em>filename/URL</em></code></td>
+ <td>Add an annotations file to the open alignment.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr>
+ <td><code>--showannotations / --noshowannotations</code></td>
+ <td>Enforces showing (or not showing) alignment annotations.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>--structure <em>filename/URL</em></code></td>
+ <td>Load a structure file attached to a sequence in the open alignment.</td>
+ <td>
+ <code>
+ seqid=<em>sequenceid</em></code> or <code><em>sequence index</em>,
+ paefile=<em>paefilename</em>,
+ tempfac=<em>temperature factor type</em>,
+ ssannotations,
+ notempfac,
+ structureviewer=<em>structure viewer</em>
+ </code></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>--paematrix <em>filename</em></code></td>
+ <td>Add a PAE file to the preceding <code>--structure</code></td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>--tempfac <em>temperature factor type</em></code></td>
+ <td>Set the type of temperature factor. Possible values are
+ <code>default</code>,
+ <code>plddt</code>
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>--structureviewer <em>structure viewer</em></code></td>
+ <td>Set the structure viewer to use to open the 3d structure file specified in previous <code>--structure</code>. Possible values are:
+ <br/>
+ <code>none</code>,
+ <br/>
+ <code>jmol</code>,
+ <br/>
+ <code>chimera</code> <em>- requires installation, might need configuring in Preferences</em>,
+ <br/>
+ <code>chimerax</code> <em>- requires installation, might need configuring in Preferences</em>,
+ <br/>
+ <code>pymol</code> <em>- requires installation, might need configuring in Preferences</em>
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>--notempfac</code></td>
+ <td>Do not show the temperature factor annotation for the preceding <code>--structure</code></td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>--groovy <em>filename</em></code></td>
+ <td>Process a groovy script in the file for the open alignment.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>--image <em>new filename</em></code></td>
+ <td>Output an image of the open alignment window. Format is specified by the subval modifier, a following <code>--type</code> argument or guessed from the file extension. Valid formats/extensions are:
+ <code>svg</code>,
+ <code>png</code>,
+ <code>eps</code>,
+ <code>html</code>,
+ <code>biojs</code>
+ </td>
+ <td>
+ <code>type=<em>image format</em>,
+ <code>textrenderer=<em>text format</em>
+ </td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr>
+ <td><code>--type <em>image format</em></code></td>
+ <td>Set the image format for the preceding <code>--image</code>. Valid values are:
+ <code>svg</code>,
+ <code>png</code>,
+ <code>eps</code>,
+ <code>html</code>,
+ <code>biojs</code>
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr>
+ <td><code>--textrenderer <em>text format</em></code></td>
+ <td>Sets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Possible values are:
+ <code>text</code>,
+ <code>lineart</code>
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr>
+ <td><code>--output <em>outputfilename</em></code></td>
+ <td>Export the open alignment. Format is specified by the subval modifier, a following <code>--format</code> argument or guessed from the file extension. Valid formats/extensions are:
+ <br/>
+ Fasta (<code>fa, fasta</code>),
+ <br/>
+
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>-- <em></em></code></td>
+ <td></td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>-- <em></em></code></td>
+ <td></td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ <tr>
+ <td><code>-- <em></em></code></td>
+ <td></td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+
+ </table>