3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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22 <title>Jalview Command Line Arguments (pre 2.11.3.0) - DEPRECATED</title>
25 <strong>The Jalview Executable's Command Line Arguments (pre 2.11.3.0) - DEPRECATED</strong>
31 This page describes the command line arguments used pre 2.11.3.0 (released mid 2023).
33 Whilst these arguments will be supported for some versions after 2.11.3.0, they are now deprecated
34 and will be removed at some time in the future.
41 <a href="commandline.html">running Jalview from the command line</a>
44 <br />Jalview processes arguments on the command line sequentially. If
45 you would like to pass a <a href="jvlfiles.html">'JVL' file</a> containing
46 <a href="../memory.html">memory settings</a> or any other launch
47 parameters, then include it at the beginning of the command line to
48 ensure they are processed before any remaining arguments.
50 Typical command line execution follows the following pattern:
52 jalview -open <Alignment File/URL> [additional import arguments] [export arguments]
55 <table width="100%" border="1" cellspacing="0" cellpadding="0">
57 <td width="27%"><div align="center">-nodisplay</div></td>
58 <td width="73%"><div align="left">Run Jalview without
59 User Interface. (automatically disables questionnaire, version
60 and usage stats checks)</div></td>
63 <td><div align="center">-nowebservicediscovery</div></td>
64 <td><div align="left">Do not query configured servers to
65 discover web services (<em>Since 2.11.2.0</em>)</div></td>
68 <td><div align="center">-open FILE/URL</div></td>
69 <td><div align="left">Specify the alignment file to
70 open or process by providing additional arguments.</div></td>
73 <td><div align="center">-props FILE/URL</div></td>
74 <td><div align="left">Use the given Jalview properties
75 file instead of users default.</div></td>
78 <td><div align="center">-setprop PROPERTY=value</div></td>
79 <td><div align="left">(JalviewJS ONLY) sets the given
80 property to the given value</div></td>
83 <td><div align="center">-features FILE/URL</div></td>
84 <td><div align="left">
86 Use the given file to add sequence features to an alignment.
87 See <a href="featuresFormat.html" target="NEW">Features
88 File</a> (Known as Groups file prior to 2.08) description.
95 <div align="center">-colour COLOURSCHEME</div>
97 <td>Set the colourscheme for the alignment. This can be any
98 of the built-in colourschemes, a name of a predefined
99 colourscheme (defined in the Jalview properties file), or an
100 'inline' colourscheme (see the applet's colour parameter for
101 more information).</td>
105 <div align="center">-annotations FILE/URL</div>
107 <td>Add precalculated annotations to the alignment. See <a
108 href="annotationsFormat.html" target="NEW">Annotation
109 File</a> description.
114 <div align="center">-no-annotation</div>
116 <td>Do not display annotation below the alignment.
122 <div align="center">-tree FILE/URL</div>
124 <div align="left">Load the given newick format tree file
125 onto the alignment</div>
130 <div align="center">-questionnaire URL</div>
132 <div align="left">Queries the given URL for information
133 about any Jalview user questionnaires</div>
138 <div align="center">-noquestionnaire</div>
140 <div align="left">Turn off questionnaire check</div>
145 <div align="center">-nonews</div>
148 Disable check for <a href="../webServices/newsreader.html">Jalview
149 news</a> on startup (not recommended other than for classroom /
156 <div align="center">-nousagestats</div>
158 <div align="left">Turn off google analytics usage tracking</div>
163 <div align="center">-[no]sortbytree</div>
165 <div align="left">Enable or disable automatic sorting of
166 associated view when a new tree is displayed</div>
171 <div align="center">-groovy FILE/URL</div>
173 <div align="left">Execute groovy script in FILE (where
174 FILE may be 'STDIN' to read from the standard input) after all
175 other arguments have been processed</div>
180 <div align="center">-jabaws URL</div>
182 <div align="left">Specify the URL of the preferred JABAWS
188 <div align="center">-fasta FILE</div>
192 <div align="left">Create alignment file FILE in Fasta
197 <td><div align="center">-clustal FILE</div></td>
198 <td><div align="left">Create alignment file FILE in
199 Clustal format.</div></td>
202 <td><div align="center">-msf FILE</div></td>
204 <td><div align="left">Create alignment file FILE in MSF
208 <td><div align="center">-pileup FILE</div></td>
209 <td><div align="left">Create alignment file FILE in
210 Pileup format.</div></td>
213 <td><div align="center">-pir FILE</div></td>
215 <td><div align="left">Create alignment file FILE in PIR
219 <td><div align="center">-pfam FILE</div></td>
220 <td><div align="left">Create alignment file FILE in
221 PFAM format.</div></td>
224 <td><div align="center">-blc FILE</div></td>
225 <td><div align="left">Create alignment file FILE in BLC
229 <td><div align="center">-json FILE</div></td>
230 <td><div align="left">Create alignment file FILE in
231 JSON format.</div></td>
234 <td><div align="center">-jalview FILE</div></td>
236 <td><div align="left">Create alignment file FILE in
237 Jalview format.</div></td>
240 <td><div align="center">-png FILE</div></td>
241 <td><div align="left">Create PNG image FILE from
242 alignment.</div></td>
245 <td><div align="center">-imgMap FILE</div></td>
247 <td><div align="left">Create HTML file FILE with image
248 map of PNG image.</div></td>
251 <td><div align="center">-eps FILE</div></td>
252 <td><div align="left">Create EPS file FILE from
253 alignment.</div></td>
256 <td><div align="center">-svg FILE</div></td>
257 <td><div align="left">Create Scalable Vector Graphics
258 file FILE from alignment.</div></td>
261 <td><div align="center">-biojsMSA FILE</div></td>
262 <td><div align="left">Write an HTML page to display
263 the alignment with the <a href="biojsmsa.html">
264 BioJS MSAviewer MSA</a>
269 <td><div align="center">-jvmmempc=PERCENT</div></td>
270 <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
271 Limit maximum heap size (memory) to PERCENT% of total physical memory detected.
272 This defaults to 90 if total physical memory can be detected.
273 See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
278 <td><div align="center">-jvmmemmax=MAXMEMORY</div></td>
279 <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
280 Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m),
281 gigabytes(g) or if you're lucky enough, terabytes(t).
282 This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected.
283 See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.