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3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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96 <li id="applet"><a href="applets.html" title="applet"></a></li>
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139 <div style="clear:both"></div>
149 <li class="jvlite-nav-title"><a href="applets.html">JalviewLite
151 <li><a href="appletParameters.html">Applet Parameters</a></li>
152 <li><a href="jalviewLiteJs.html">Javascript API</a></li>
153 <li><a href="formComplete.html">in-page API demo</a></li>
154 <li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
155 <li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
159 <div id="content" class="content">
160 <p>JalviewLite is a web based version of Jalview, which runs as a
161 Java applet in or on a web page. It's one of the easiest ways of
162 providing an interactive display for precalculated alignments,
163 features and annotations files. It lacks some functionality
164 available in the Jalview Desktop, however, such as making images,
165 saving files, and running web service jobs. This is mostly due to
166 security restrictions imposed on applets.</p>
168 Try out JalviewLite by pressing one of the buttons below. For more information on how to use the applet in your website, see the <a
169 href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
172 <h2>Ferredoxins, chloroplast precursor related UniRef50
174 <br /> (15 sequences x 150 residues)
178 <td width="10%" valign="center"><applet
179 code="jalview.bin.JalviewLite" width="140" height="35"
180 archive="jalviewApplet.jar">
181 <param name="file" value="uniref50.fa">
182 <param name="treeFile" value="ferredoxin.nw">
183 <param name="userDefinedColour"
184 value="C=yellow; R,K,H=FF5555; D,E=5555FF">
185 <param name="showFullId" value="false">
186 <param name="sortByTree" value="True">
187 <param name="showSequenceLogo" value="true">
188 <param name="showGroupConsensus" value="true">
189 <param name="linkLabel_1" value="Uniprot">
190 <param name="linkUrl_1"
191 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
192 <param name="linkLabel_2" value="Expasy">
193 <param name="linkUrl_2"
194 value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
195 <param name="APPLICATION_URL"
196 value="http://www.jalview.org/services/launchApp">
198 <td valign="center">User Defined Colours, loads an associated
199 Newick format tree file which is used to sort the alignment, and
200 group consensus and sequence logos are shown below the alignment.</td>
203 <td width="10%" valign="center"><applet
204 code="jalview.bin.JalviewLite" width="140" height="35"
205 archive="jalviewApplet.jar">
206 <param name="file" value="uniref50.fa">
207 <param name="features" value="exampleFeatures.txt">
208 <param name="showFeatureSettings" value="true">
209 <param name="wrap" value="true">
210 <param name="showAnnotation" value="false">
211 <param name="windowHeight" value="500">
212 <param name="windowWidth" value="650">
213 <param name="showFullId" value="false">
214 <param name="linkLabel_1" value="Uniprot">
215 <param name="linkUrl_1"
216 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
217 <param name="linkLabel_2" value="Expasy">
218 <param name="linkUrl_2"
219 value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
220 <param name="APPLICATION_URL"
221 value="http://www.jalview.org/services/launchApp">
223 <td valign="center">Displays a features file on the alignment</td>
226 <td width="10%" valign="center"><applet
227 code="jalview.bin.JalviewLite" width="140" height="35"
228 archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
229 <param name="file" value="uniref50.fa">
230 <!-- <param name="debug" value="true">
232 <param name="defaultColour" value="Strand Propensity">
233 <param name="wrap" value="true">
234 <param name="showAnnotation" value="false">
235 <param name="windowHeight" value="500">
236 <param name="windowWidth" value="650">
237 <param name="showFullId" value="false">
238 <param name="linkLabel_1" value="Uniprot">
239 <param name="linkUrl_1"
240 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
241 <param name="linkLabel_2" value="Expasy">
242 <param name="linkUrl_2"
243 value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
244 <param name="APPLICATION_URL"
245 value="http://www.jalview.org/services/launchApp">
246 <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
248 <td valign="center">Associates PDB file 1GAQ with sequence
252 <td width="10%" valign="middle"><applet
253 code="jalview.bin.JalviewLite" width="140" height="35"
254 archive="jalviewApplet.jar">
255 <param name="file" value="jpred_msa.fasta">
256 <param name="jnetfile" value="jpred_msa.seq.concise">
257 <param name="defaultColour" value="Clustal">
258 <param name="showAnnotation" value="true">
259 <param name="windowHeight" value="515">
260 <param name="windowWidth" value="650">
261 <param name="showConservation" value="false">
262 <param name="showQuality" value="false">
263 <param name="showConsensus" value="false">
264 <param name="showFullId" value="false">
265 <param name="linkLabel_1" value="Uniprot">
266 <param name="linkUrl_1"
267 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
268 <param name="linkLabel_2" value="Expasy">
269 <param name="linkUrl_2"
270 value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
271 <param name="APPLICATION_URL"
272 value="http://www.jalview.org/services/launchApp">
274 <td valign="center">Displays a Multiple Sequence Alignment
275 Based JNet Prediction for a Sequence</td>
279 <h2>RF00031 RFAM Alignment with per sequence secondary
284 <td width="10%" valign="center"><applet
285 code="jalview.bin.JalviewLite" width="140" height="35"
286 archive="jalviewApplet.jar">
287 <param name="file" value="RF00031_folded.stk">
288 <param name="defaultColour" value="Purine/Pyrimidine">
289 <param name="showAnnotation" value="true">
290 <param name="windowHeight" value="515">
291 <param name="windowWidth" value="650">
292 <param name="showConservation" value="false">
293 <param name="showQuality" value="false">
294 <param name="showConsensus" value="true">
295 <param name="showFullId" value="false">
296 <param name="APPLICATION_URL"
297 value="http://www.jalview.org/services/launchApp">
299 <td valign="center">Displays an RFAM RNA fold family with
300 secondary structure annotation</td>
308 <div id="innerFooter">
309 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
312 If you use Jalview in your work, please cite this publication:
316 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
317 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
318 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>