2 <title>Jalview Command Line Arguments
5 <p><strong>The Jalview Executable's Command Line
7 See <a href="commandline.html">running Jalview from the command
8 line</a> for more information.<br>
9 <table width="100%" border="1" cellspacing="0" cellpadding="0">
11 <td width="27%"><div align="center">-nodisplay</div></td>
12 <td width="73%"><div align="left">Run Jalview without User Interface.</div></td>
16 <td><div align="center">-props FILE</div></td>
17 <td><div align="left">Use the given Jalview properties file instead
18 of users default.</div></td>
21 <td><div align="center">-features FILE</div></td>
22 <td><div align="left">
23 <p>Use the given file to add sequence features to an alignment.
24 See <a href="featuresFormat.html" target="NEW">Features
25 File</a> (Known as Groups file prior to 2.08) description. </p>
30 <td><div align="center">-annotations FILE</div></td>
31 <td>Add precalculated annotations to the alignment. See <a href="annotationsFormat.html" target="NEW">Annotation
32 File</a> description.</td>
35 <td><div align="center">-fasta FILE</div></td>
37 <td><div align="left">Create alignment file FILE in Fasta format.</div></td>
40 <td><div align="center">-clustal FILE</div></td>
41 <td><div align="left">Create alignment file FILE in Clustal format.</div></td>
44 <td><div align="center">-msf FILE</div></td>
46 <td><div align="left">Create alignment file FILE in MSF format.</div></td>
49 <td><div align="center">-pileup FILE</div></td>
50 <td><div align="left">Create alignment file FILE in Pileup format.</div></td>
53 <td><div align="center">-pir FILE</div></td>
55 <td><div align="left">Create alignment file FILE in PIR format.</div></td>
58 <td><div align="center">-blc FILE</div></td>
59 <td><div align="left">Create alignment file FILE in BLC format.</div></td>
62 <td><div align="center">-jalview FILE</div></td>
64 <td><div align="left">Create alignment file FILE in Jalview format.</div></td>
67 <td><div align="center">-png FILE</div></td>
68 <td><div align="left">Create PNG image FILE from alignment.</div></td>
71 <td><div align="center">-imgMap FILE</div></td>
73 <td><div align="left">Create HTML file FILE with image map of PNG
77 <td><div align="center">-eps FILE</div></td>
78 <td><div align="left">Create EPS file FILE from alignment.</div></td>