-<html>\r
-<head>\r
-<title>Exporting alignments as artwork</title>\r
-</head>\r
-<body>\r
-<p><strong>Exporting alignments as graphics and lineart<a name="export"></a></strong></p>\r
-<p>The alignment view can be printed using\r
-<strong>File→Print</strong>, or exported in a number of ways via the\r
-<strong>File→Export</strong> menu:\r
-<ul>\r
-<li>HTML<br><em>for viewing in a web browser</em>\r
-</li>\r
-<li>PNG - a Portable Networks Graphics image<br><em>For low quality\r
-diagrams and powerpoint presentations</em>\r
-</li>\r
-<li>EPS - an Encapsulated Postscript Document<br><em>For high quality\r
-diagrams and publications.</em>\r
-</li></ul>\r
- \r
-<p><em>Tips for working with EPS Files</em></p>\r
-<li>The EPS file generated by jalview contains vector graphics which are directly \r
- editable in graphics applications such as Adobe Illustrator.</li>\r
-<li>EPS files can be produced as "Text" or "Lineart". Use \r
- "Text" if you want the final document to be MUCH smaller in diskspace \r
- and be able to search, edit and select text. Use "Lineart" if you \r
- want an exact image of the alignment as displayed in Jalview. This is useful \r
- if a 3rd Party EPS viewer does not have the same Font which the EPS file was \r
- created with.</li>\r
-<li>When importing an EPS into to a Microsoft office document, a snapshot image of the\r
- file will be displayed which often looks blurred. Right-click the\r
- image and choose "Edit image." to convert it to word\r
- drawing objects which give a truer WYSIWIG representation.\r
- </li>\r
- <li>\r
- Mac OSX users will find that eps files are automatically converted into\r
- PDF files. \r
- </li>\r
-</p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * 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
+ * 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.
+ -->
+<head>
+<title>Exporting alignments as artwork</title>
+</head>
+<body>
+ <p>
+ <strong>Exporting alignments as graphics and lineart<a
+ name="export"
+ ></a></strong>
+ </p>
+ <p>
+ The alignment view can be printed using <strong>File→Print</strong>,
+ or exported in a number of ways via the <strong>File→Export</strong>
+ menu:
+ <ul>
+ <li>HTML<br> <em>for viewing in a web browser</em>
+ </li>
+ <li>PNG - a Portable Networks Graphics image<br> <em>For
+ low quality diagrams and powerpoint presentations</em>
+ </li>
+ <li>EPS - an Encapsulated Postscript Document<br> <em>For
+ high quality diagrams and publications.</em>
+ <li>SVG - a Scalable Vector Graphics document<br> <em>For
+ high quality diagrams in publications and on the web.</em>
+ </li>
+ <li>BioJS MSA - A JavaScript based multiple sequence alignment
+ viewer. <br> <em>For interactive alignment data
+ visualisation in a web browser.<br />Get more info about the
+ BioJS MSA viewer at <a href="http://msa.biojs.net/">http://msa.biojs.net/</a>
+ </em>
+ </li>
+
+ </ul>
+ <a name="htmlexport" />
+ <p>
+ <strong>Exporting alignments as Web Pages</strong>
+ <p>
+ In Jalview 2.9, new HTML exporting options were introduced. The
+ standard HTML export option displays alignments as SVG documents
+ embedded as scrollable panes. Exported pages can optionally also
+ include <a href="../features/bioJsonFormat.html">BioJSON</a> data,
+ which allows Jalview to extract the original data used to create the
+ page. Jalview can also generate HTML pages which embed BioJSON data
+ and the BioJS MSA viewer, a pure javascript alignment viewer that
+ provides a range of interactive analysis capabilities.
+ </p>
+ <p>
+ <p>
+ <strong>Tips for working with EPS Files</strong>
+ </p>
+ <li>The EPS file generated by Jalview contains vector graphics
+ which are directly editable in graphics applications such as Adobe
+ Illustrator.</li>
+ <li>EPS files can be produced as "Text" or
+ "Lineart". Use "Text" if you want the final
+ document to be MUCH smaller in diskspace and be able to search, edit
+ and select text. Use "Lineart" if you want an exact image
+ of the alignment as displayed in Jalview. This is useful if a 3rd
+ Party EPS viewer does not have the same Font which the EPS file was
+ created with.</li>
+ <li>When importing an EPS file into a Microsoft office document,
+ a snapshot image of the file will be displayed which often looks
+ blurred. Right-click the image and choose "Edit image." to
+ convert it to word drawing objects which give a truer WYSIWIG
+ representation.</li>
+ <li>Mac OSX users will find that eps files are automatically
+ converted into PDF files.</li>
+ </p>
+</body>
+</html>