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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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146 <li class="jvlite-nav-title"><a href="applets.html">JalviewLite
148 <li><a href="appletParameters.html">Applet Parameters</a></li>
149 <li><a href="jalviewLiteJs.html">Javascript API</a></li>
150 <li><a href="formComplete.html">in-page API demo</a></li>
151 <li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
152 <li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
156 <div id="content" class="content">
157 <p>JalviewLite is a web based version of Jalview, which runs as a
158 Java applet in or on a web page. It's one of the easiest ways of
159 providing an interactive display for precalculated alignments,
160 features and annotations files. It lacks some functionality
161 available in the Jalview Desktop, however, such as making images,
162 saving files, and running web service jobs. This is mostly due to
163 security restrictions imposed on applets.</p>
165 For more information on how to use the applet in your website, see <a
166 href="appletParameters.html"><strong>full list of
168 <p>Pressing one of the buttons below will load up JalviewLite,
169 a cut down version parameters.
172 of Jalview, which runs within your web browser.
176 <h2>Ferredoxins, chloroplast precursor related UniRef50
178 <br /> (15 sequences x 150 residues)
182 <td width="10%" valign="center"><applet
183 code="jalview.bin.JalviewLite" width="140" height="35"
184 archive="jalviewApplet.jar">
185 <param name="file" value="uniref50.fa">
186 <param name="treeFile" value="ferredoxin.nw">
187 <param name="userDefinedColour"
188 value="C=yellow; R,K,H=FF5555; D,E=5555FF">
189 <param name="showFullId" value="false">
190 <param name="sortByTree" value="True">
191 <param name="showSequenceLogo" value="true">
192 <param name="showGroupConsensus" value="true">
193 <param name="linkLabel_1" value="Uniprot">
194 <param name="linkUrl_1"
195 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
196 <param name="linkLabel_2" value="Expasy">
197 <param name="linkUrl_2"
198 value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
199 <param name="APPLICATION_URL"
200 value="http://www.jalview.org/services/launchApp">
202 <td valign="center">User Defined Colours, loads an associated
203 Newick format tree file which is used to sort the alignment, and
204 group consensus and sequence logos are shown below the alignment.</td>
207 <td width="10%" valign="center"><applet
208 code="jalview.bin.JalviewLite" width="140" height="35"
209 archive="jalviewApplet.jar">
210 <param name="file" value="uniref50.fa">
211 <param name="features" value="exampleFeatures.txt">
212 <param name="showFeatureSettings" value="true">
213 <param name="wrap" value="true">
214 <param name="showAnnotation" value="false">
215 <param name="windowHeight" value="500">
216 <param name="windowWidth" value="650">
217 <param name="showFullId" value="false">
218 <param name="linkLabel_1" value="Uniprot">
219 <param name="linkUrl_1"
220 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
221 <param name="linkLabel_2" value="Expasy">
222 <param name="linkUrl_2"
223 value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
224 <param name="APPLICATION_URL"
225 value="http://www.jalview.org/services/launchApp">
227 <td valign="center">Displays a features file on the alignment</td>
230 <td width="10%" valign="center"><applet
231 code="jalview.bin.JalviewLite" width="140" height="35"
232 archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
233 <param name="file" value="uniref50.fa">
234 <!-- <param name="debug" value="true">
236 <param name="defaultColour" value="Strand Propensity">
237 <param name="wrap" value="true">
238 <param name="showAnnotation" value="false">
239 <param name="windowHeight" value="500">
240 <param name="windowWidth" value="650">
241 <param name="showFullId" value="false">
242 <param name="linkLabel_1" value="Uniprot">
243 <param name="linkUrl_1"
244 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
245 <param name="linkLabel_2" value="Expasy">
246 <param name="linkUrl_2"
247 value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
248 <param name="APPLICATION_URL"
249 value="http://www.jalview.org/services/launchApp">
250 <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
252 <td valign="center">Associates PDB file 1GAQ with sequence
256 <td width="10%" valign="middle"><applet
257 code="jalview.bin.JalviewLite" width="140" height="35"
258 archive="jalviewApplet.jar">
259 <param name="file" value="jpred_msa.fasta">
260 <param name="jnetfile" value="jpred_msa.seq.concise">
261 <param name="defaultColour" value="Clustal">
262 <param name="showAnnotation" value="true">
263 <param name="windowHeight" value="515">
264 <param name="windowWidth" value="650">
265 <param name="showConservation" value="false">
266 <param name="showQuality" value="false">
267 <param name="showConsensus" value="false">
268 <param name="showFullId" value="false">
269 <param name="linkLabel_1" value="Uniprot">
270 <param name="linkUrl_1"
271 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
272 <param name="linkLabel_2" value="Expasy">
273 <param name="linkUrl_2"
274 value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
275 <param name="APPLICATION_URL"
276 value="http://www.jalview.org/services/launchApp">
278 <td valign="center">Displays a Multiple Sequence Alignment
279 Based JNet Prediction for a Sequence</td>
283 <h2>RF00031 RFAM Alignment with per seqeunce secondary
288 <td width="10%" valign="center"><applet
289 code="jalview.bin.JalviewLite" width="140" height="35"
290 archive="jalviewApplet.jar">
291 <param name="file" value="RF00031_folded.stk">
292 <param name="defaultColour" value="Purine/Pyrimidine">
293 <param name="showAnnotation" value="true">
294 <param name="windowHeight" value="515">
295 <param name="windowWidth" value="650">
296 <param name="showConservation" value="false">
297 <param name="showQuality" value="false">
298 <param name="showConsensus" value="true">
299 <param name="showFullId" value="false">
300 <param name="APPLICATION_URL"
301 value="http://www.jalview.org/services/launchApp">
303 <td valign="center">Displays an RFAM RNA fold family with
304 secondary structure annotation</td>
312 <div id="innerFooter">
313 <div id="copyright"><p>Copyright all rights reserved 2012</p></div>
316 If you use Jalview in your work, please cite this publication:
320 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
321 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
322 Bioinformatics 25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp033