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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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/>.
+ * 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>What's new ?</title>
</head>
<body>
- <p>
- <strong>What's new ?</strong><br /> Jalview 2.8.1 includes a range of new features developed in the last 12 months. <br /> As usual you can find the
- highlights below, and the comprehensive list is given in the <a
- href="releases.html#Jalview2.8.1">Jalview 2.8.1 Release Notes</a>.
- </p>
- <strong>Internationalisation</strong>
- <p>
- In August 2013, David Róldan-Martinez took on the task of
- internationalising Jalview's user interface. He also recruited Sara
- Hernández Díaz and Laura Ferrandis Martinez who created Jalview's
- first spanish user interface translation.<br /> If you notice any
- problems, or would like to help translate Jalview's user interface
- into other languages, head over to <a href="http://issues.jalview.org">issues.jalview.org</a>
- and put in a feature request describing the translations you can
- provide to the <a
- href="http://issues.jalview.org/browse/JAL/component/10682">i18n
- component</a>.<br/>
- David has also put together some documentation about getting started with i18n translations
- </p>
- <strong>Enhancements and new features</strong>
- <ul>
- <li>
- <li>Extended the feature settings dialog to <a href="features/featuresettings.html#selectbyfeature">select columns containing particular sequence features.</a></li>
- </ul>
- <strong>Bug fixes</strong>
- <ul>
- </ul>
+ <p>
+ <strong>What's new ?</strong>
+ </p>
+ <p>
+ Jalview 2.9 has been in development since December 2014. In addition
+ to a multitude of bug fixes and minor improvements (both small, and
+ rather big!), it also brings major new capabilities for codon-level
+ analysis of protein alignments and the retrieval and manipulation of
+ structural data.</p><p>For the full list of changes, see the
+ <a href="releases.html#Jalview.2.9">Jalview 2.9 Release Notes</a>.
+ </p>
+ <p>
+ <strong>Highlights in Jalview 2.9</strong>
+ <ul>
+ <li><strong>Visualisation, editing and analysis of
+ cDNA and Protein alignments</strong><br />A new <a
+ href="features/splitView.html">Split View</a> window allows linked
+ protein and nucleotide sequence alignments to be viewed, edited,
+ and analysed as one. <br />cDNA alignments can also be
+ reconstructed from protein alignments calculated by Jalview's web
+ services, and update in response to edits in the amino acid view.<br />To
+ start experimenting with cDNA/Protein analysis, jut drop a file
+ containing cDNA sequences which code for proteins in an existing
+ alignment, and Jalview will do the rest.</li>
+ <li><strong>Enhanced Integration of UCSF Chimera</strong> <br>Jalview
+ 2.9 provides full support for the use of Chimera to view 3D
+ structures linked to alignment views in the Jalview Desktop. We've
+ also included support for saving Chimera sessions in Jalview
+ project files.<br />Jalview and Chimera communicate using local
+ web server connections, which may cause firewall alerts on some
+ systems, but has the advantage of allowing bidirectional
+ communication. Communication between Jalview and Chimera is now
+ much more responsive, and selected regions in Chimera are now
+ shown as highlighted regions in the Jalview desktop.</li>
+ <li><strong>Interactive querying of the PDBe</strong><br />Jalview
+ users can now <a href="features/pdbsequencefetcher.html">browse</a> and <a href="features/viewingpdbs.html">retrieve 3D structure</a> data from the PDB
+ via the <a href="http://www.ebi.ac.uk/pdbe/api/doc/search.html">PDBe
+ Search API</a> (<a href="http://dx.doi.org/10.1093%2Fnar%2Fgkt1180">Gutmanas
+ et al 2014</a>). Developed in collaboration with the PDBe group at
+ EMBL-EBI, the interface allows both structured and free-text
+ queries to be performed, and allows automatic selection of the
+ most relevant structures for an alignment acording to a variety of
+ criteria.</li>
+ <li><strong>Improved support for RNA visualisation</strong><br />Jalview
+ 2.9 integrates the latest version of the <a
+ href="features/varna.html">VARNA RNA Viewer</a>, and VARNA views
+ can also now be stored in Jalview projects. We've also dealt with
+ a number of lingering bugs in the VARNA/Jalview interface,
+ including the loss of pseudoknots when RNA secondary structure is
+ shown VARNA.</li>
+ <li><strong>Protein Secondary Structure predictions
+ with JPred4</strong><br />Jalview includes a number of new features for
+ working with secondary structure predictions from the JPred4
+ server. These include new <a href="menus/popupMenu.html#hideinserts">popup menu actions</a> to automatically hide insertions and highlight
+ mutations in an alignment with respect to a <a href="calculations/referenceseq.html">Reference
+ Sequence</a>. Jalview 2.9's new <a href="io/export.html#htmlexport">scrollable
+ SVG HTML export</a> was also developed specifically for the JPred4
+ server.</li>
+ </ul>
+
</body>
</html>
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