<html>
+<!--
+ *Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ *Copyright (C) 2015 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
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+ *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'. 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>
+ 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 exports uses the latest
+ <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