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>
31 <div align="center">-annotations FILE</div>
33 <td>Add precalculated annotations to the alignment. See <a
34 href="annotationsFormat.html" target="NEW">Annotation File</a>
39 <div align="center"></div>
41 <div align="left"></div>
46 <div align="center">-nodisplay</div>
48 <div align="left">Run Jalview without User Interface</div>
53 <div align="center">-props FILE</div>
55 <div align="left">Use the given Jalview properties file instead
56 of users default</div>
61 <div align="center">-tree FILE</div>
63 <div align="left">Load the given newick format tree file onto
69 <div align="center">-features FILE</div>
71 <div align="left">Use the given file to mark features on the
77 <div align="center">-questionnaire URL</div>
79 <div align="left">Queries the given URL for information about
80 any Jalview user questionnaires</div>
85 <div align="center">-noquestionnaire</div>
87 <div align="left">Turn off questionnaire check</div>
92 <div align="center">-dasserver nickname=URL</div>
94 <div align="left">Add and enable a das server with given
95 nickname (alphanumeric or underscores only) for retrieval of features
96 for all alignments</div>
101 <div align="center">-fetchfrom nickname</div>
103 <div align="left">Query nickname for features for the alignments
104 and display them</div>
109 <div align="center">-groovy FILE</div>
111 <div align="left">Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
112 arguments have been processed</div>
117 <div align="center">-fasta FILE</div>
121 <div align="left">Create alignment file FILE in Fasta format.</div>
125 <td><div align="center">-clustal FILE</div></td>
126 <td><div align="left">Create alignment file FILE in Clustal format.</div></td>
129 <td><div align="center">-msf FILE</div></td>
131 <td><div align="left">Create alignment file FILE in MSF format.</div></td>
134 <td><div align="center">-pileup FILE</div></td>
135 <td><div align="left">Create alignment file FILE in Pileup format.</div></td>
138 <td><div align="center">-pir FILE</div></td>
140 <td><div align="left">Create alignment file FILE in PIR format.</div></td>
143 <td><div align="center">-pfam FILE</div></td>
144 <td><div align="left">Create alignment file FILE in PFAM format.</div></td>
147 <td><div align="center">-blc FILE</div></td>
148 <td><div align="left">Create alignment file FILE in BLC format.</div></td>
151 <td><div align="center">-jalview FILE</div></td>
153 <td><div align="left">Create alignment file FILE in Jalview format.</div></td>
156 <td><div align="center">-png FILE</div></td>
157 <td><div align="left">Create PNG image FILE from alignment.</div></td>
160 <td><div align="center">-imgMap FILE</div></td>
162 <td><div align="left">Create HTML file FILE with image map of PNG
166 <td><div align="center">-eps FILE</div></td>
167 <td><div align="left">Create EPS file FILE from alignment.</div></td>