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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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 includes a number of enhancements and new features that
- have been in development since July 2010. It is also the first Jalview
- release to incorporate RNA visualization features developed by Lauren
- Lui and Jan Engelhart during their Google Summer of Code projects
- (http://code.google.com/soc/). As usual you can find the highlights
- below, but to see the comprehensive list take a look at the look at
- the <a href="releases.html#Jalview2.8">Jalview 2.8 Release Notes</a>.
- </p>
- <strong>Highlights in Jalview Version 2.8</strong>
- <ul>
- <li><strong>Improved <a href="webServices/JABAWS.html">JABAWS</a>
- client and new JABAWS 2.0 Services
- </strong>
- <ul>
- <li><a href="webServices/AACon.html">AACon alignment
- conservation</a></li>
- <li><a href="webServices/proteinDisorder.html">Protein
- disorder</a> - DisEMBL, RONN, GlobPlot and IUPred</li>
- <li>Clustal Omega for creating huge protein alignments</li>
- </ul></li>
- <li><strong><a href="na/index.html">RNA</a></strong>
- <ul>
- <li>Import sequence and alignment associated WUSS or VIENNA
- dot-bracket notation from files and the <strong>RFAM</strong>
- database
- </li>
- <li>Interactive editing of RNA secondary structure annotation</li>
- <li>Colour scheme for purine/pyrimidine and to highlight RNA
- helices</li>
- <li>RNA canonical <a
- href="calculations/structureconsensus.html">base pair consensus
- score</a> and sequence logo
- </li>
- <li>Embedded <a href="features/varna.html">VARNA</a> RNA
- secondary structure viewer in the Desktop
- </li>
- </ul></li>
- <li>Parse and display <a href="io/tcoffeescores.html">T-COFFEE
- alignment quality scores</a> (thanks to Paolo di Tomasso of the Notredame
- Group)
- </li>
- <li><a href="colourSchemes/annotationColouring.html">Per
- sequence alignment annotation shading</a></li>
- <li>Enhanced <a href="calculations/pca.html">PCA viewer</a>: more
- export options, and switch between different PCA modes and residue
- score models
- </li>
- <li>New Jalview Desktop <a href="webServices/dbreffetcher.html">database
- fetcher</a> GUI
- </li>
- <li>Support for DAS 1.6 and DAS 2.0 sources (thanks to the new
- JDAS Distributed Annotation client library (see
- http://code.google.com/p/jdas))</li>
- <li>Export sequence database annotation as an <a
- href="io/exportseqreport.html">HTML report</a></li>
- <li>Normalised <a href="calculations/consensus.html">Sequence
- Logo Display</a></li>
- </ul>
- <p>
- <strong>Issues resolved in the Jalview Desktop</strong>
- </p>
- <ul>
- <li>PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch
- REST service</li>
- <li>Stop windows being moved outside desktop on OSX</li>
- <li>Jnet job queues forever if a very short sequence is submitted
- for prediction</li>
- <li>Structure view highlighting doesn't work on windows 7</li>
- <li>Jalview desktop fails to launch with exception when using
- proxy</li>
- <li>DAS Sequence retrieval with range qualification results in
- sequence xref which includes range qualification</li>
- <li>Cannot close news reader when JABAWS server warning dialog is
- shown</li>
- <li>Edited sequence not submitted to web service</li>
- <li>Jalview 2.7 InstallAnywhere installer doesn't unpack and run
- on OSX Mountain Lion
- <ul>
- <li>If you use webstart then you may need to go into the
- Security panel (<em>a.k.a</em> the gatekeeper) in your System
- Settings, and select the 'allow any code to run' option.
- </li>
- </ul>
- </li>
- </ul>
- <p>
- <strong>Issues specific to the JalviewLite Applet</strong>
- </p>
- <ul>
- <li>Sequence features are momentarily displayed before they are
- hidden using hidefeaturegroups applet parameter</li>
- <li>loading features via javascript API automatically enables
- feature display</li>
- <li>scrollToColumnIn javascript API method doesn't work</li>
- </ul>
- <p>
- <strong>Issues affecting both applet and application</strong>
- </p>
- <ul>
- <li>Redundancy removal fails for rna alignment</li>
- <li>PCA window shows grey box when first opened on OSX</li>
- <li>Letters coloured pink in sequence logo when alignment
- coloured with clustalx</li>
- </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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