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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 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
166 href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
169 <h2>Ferredoxins, chloroplast precursor related UniRef50
171 <br /> (15 sequences x 150 residues)
175 <td width="10%" valign="center"><applet
176 code="jalview.bin.JalviewLite" width="140" height="35"
177 archive="jalviewApplet.jar">
178 <param name="file" value="uniref50.fa">
179 <param name="treeFile" value="ferredoxin.nw">
180 <param name="userDefinedColour"
181 value="C=yellow; R,K,H=FF5555; D,E=5555FF">
182 <param name="showFullId" value="false">
183 <param name="sortByTree" value="True">
184 <param name="showSequenceLogo" value="true">
185 <param name="showGroupConsensus" value="true">
186 <param name="linkLabel_1" value="Uniprot">
187 <param name="linkUrl_1"
188 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
189 <param name="linkLabel_2" value="Expasy">
190 <param name="linkUrl_2"
191 value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
192 <param name="APPLICATION_URL"
193 value="http://www.jalview.org/services/launchApp">
195 <td valign="center">User Defined Colours, loads an associated
196 Newick format tree file which is used to sort the alignment, and
197 group consensus and sequence logos are shown below the alignment.</td>
200 <td width="10%" valign="center"><applet
201 code="jalview.bin.JalviewLite" width="140" height="35"
202 archive="jalviewApplet.jar">
203 <param name="file" value="uniref50.fa">
204 <param name="features" value="exampleFeatures.txt">
205 <param name="showFeatureSettings" value="true">
206 <param name="wrap" value="true">
207 <param name="showAnnotation" value="false">
208 <param name="windowHeight" value="500">
209 <param name="windowWidth" value="650">
210 <param name="showFullId" value="false">
211 <param name="linkLabel_1" value="Uniprot">
212 <param name="linkUrl_1"
213 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
214 <param name="linkLabel_2" value="Expasy">
215 <param name="linkUrl_2"
216 value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
217 <param name="APPLICATION_URL"
218 value="http://www.jalview.org/services/launchApp">
220 <td valign="center">Displays a features file on the alignment</td>
223 <td width="10%" valign="center"><applet
224 code="jalview.bin.JalviewLite" width="140" height="35"
225 archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
226 <param name="file" value="uniref50.fa">
227 <!-- <param name="debug" value="true">
229 <param name="defaultColour" value="Strand Propensity">
230 <param name="wrap" value="true">
231 <param name="showAnnotation" value="false">
232 <param name="windowHeight" value="500">
233 <param name="windowWidth" value="650">
234 <param name="showFullId" value="false">
235 <param name="linkLabel_1" value="Uniprot">
236 <param name="linkUrl_1"
237 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
238 <param name="linkLabel_2" value="Expasy">
239 <param name="linkUrl_2"
240 value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
241 <param name="APPLICATION_URL"
242 value="http://www.jalview.org/services/launchApp">
243 <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
245 <td valign="center">Associates PDB file 1GAQ with sequence
249 <td width="10%" valign="middle"><applet
250 code="jalview.bin.JalviewLite" width="140" height="35"
251 archive="jalviewApplet.jar">
252 <param name="file" value="jpred_msa.fasta">
253 <param name="jnetfile" value="jpred_msa.seq.concise">
254 <param name="defaultColour" value="Clustal">
255 <param name="showAnnotation" value="true">
256 <param name="windowHeight" value="515">
257 <param name="windowWidth" value="650">
258 <param name="showConservation" value="false">
259 <param name="showQuality" value="false">
260 <param name="showConsensus" value="false">
261 <param name="showFullId" value="false">
262 <param name="linkLabel_1" value="Uniprot">
263 <param name="linkUrl_1"
264 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
265 <param name="linkLabel_2" value="Expasy">
266 <param name="linkUrl_2"
267 value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
268 <param name="APPLICATION_URL"
269 value="http://www.jalview.org/services/launchApp">
271 <td valign="center">Displays a Multiple Sequence Alignment
272 Based JNet Prediction for a Sequence</td>
276 <h2>RF00031 RFAM Alignment with per sequence secondary
281 <td width="10%" valign="center"><applet
282 code="jalview.bin.JalviewLite" width="140" height="35"
283 archive="jalviewApplet.jar">
284 <param name="file" value="RF00031_folded.stk">
285 <param name="defaultColour" value="Purine/Pyrimidine">
286 <param name="showAnnotation" value="true">
287 <param name="windowHeight" value="515">
288 <param name="windowWidth" value="650">
289 <param name="showConservation" value="false">
290 <param name="showQuality" value="false">
291 <param name="showConsensus" value="true">
292 <param name="showFullId" value="false">
293 <param name="APPLICATION_URL"
294 value="http://www.jalview.org/services/launchApp">
296 <td valign="center">Displays an RFAM RNA fold family with
297 secondary structure annotation</td>
305 <div id="innerFooter">
306 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
309 If you use Jalview in your work, please cite this publication:
313 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
314 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
315 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>