--- /dev/null
+<html>
+<!--
+ *Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ *Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ *This file is part of Jalview.
+ *
+ *Jalview is free software: you can redistribute it and/or
+ *modify it under the terms of the GNU General Public License
+ *as published by the Free Software Foundation, either version 3
+ *of the License, or (at your option) any later version.
+ *
+ *Jalview is distributed in the hope that it will be useful, but
+ *WITHOUT ANY WARRANTY; without even the implied warranty
+ *of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *PURPOSE. See the GNU General Public License for more details.
+ *
+ *You should have received a copy of the GNU General Public License
+ *along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ *The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<title>BioJS MSA Viewer Export</title>
+<body>
+ <p>
+ <strong>Exporting Alignments for viewing with the BioJS MSA
+ Viewer</strong>
+ </p>
+ <p>
+ Since Jalview 2.9, HTML files can be generated from an alignment
+ within the Jalview desktop application that show the alignment in an
+ interactive viewer called 'BioJS-MSA'. These pages embed Jalview's
+ alignment data as <a href="bioJsonFormat.html">BioJSON</a>, which
+ can be imported back into Jalview, and also interpreted by the BioJS
+ MSA viewer. The BioJS MSA Viewer is a full-featured JavaScript based
+ multiple sequence alignment visualisation system created by a
+ community of biological data visualisation developers, and is
+ developed independently of Jalview.
+ </p>
+ <p>
+ To find out more about the BioJS MSA Viewer, please go to <a
+ href="http://msa.biojs.net/">http://msa.biojs.net/</a>.
+ </p>
+
+ <p>
+ <strong>Making sure your BioJS MSA export uses the latest
+ BioJS MSA Viewer</strong>
+ </p>
+ <p>In order to allow Jalview to export data with the latest
+ version of the MSA viewer, the Jalview Desktop will download
+ templates for HTML export from our public GitHub Repository.
+ Normally, this should happen without you needing to do anything, but
+ if you do encounter problems, then please get in contact via the
+ jalview-discuss mailing list, or file a bug report.</p>
+ <p>Templates are downloaded to a directory called
+ '.biojs_templates' in your user's home storage space (e.g.
+ ~/.biojs_templates).</p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff