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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * 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>
- </p>
- <p>
- The Jalview 2.7 release features new web services, and important
- improvements to the way in which Jalview handles alignments and
- associated PDB structures, as well as numerous minor improvements and
- bug fixes. Version 2.7 of the JalviewLite applet also features a
- significantly enhanced Javascript API enabling it to be more easily
- integrated with javascript based web applications. <br /> For full
- details see the <a href="releases.html#Jalview2.7">Jalview 2.7
- release history</a>.
- </p>
- <p>
- <strong>Highlights in Jalview Desktop Version 2.7</strong>
- </p>
- <ul>
- <li>New <a href="features/viewingpdbs.html">structure viewer
- options</a>:
- <ul>
- <li>Colour and superimpose 3D structures of complexes and
- multi-domain chains using several different alignments</li>
- <li>Drag and drop to associate PDB files with sequences that
- have the same name</li>
- <li>Open and superimpose all associated structures for the
- current selection</li>
- </ul>
- <li>New web services for <a href="webServices/shmr.html">alignment
- analysis</a></li>
- <li>Improved graphical user interface for <a
- href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>services.
- </li>
- <li>Sort associated alignment views option in tree viewer</li>
- <li>Default colours for <a
- href="colourSchemes/annotationColouring.html">shading alignment
- by quantitative annotation</a>.
- </li>
- <li><a href="webServices/newsreader.html">Jalview Desktop RSS
- reader</a> - following important updates at <a
- href="http://www.jalview.org/feeds/desktop/rss">http://www.jalview.org/feeds/desktop/rss</a>
- </ul>
+ <p>
+ <strong>What's new ?</strong>
+ </p>
+ <p>
+ Jalview 2.9.0b2 is a bug fix release for Jalview 2.9.
+ The release of Jalview 2.9 in September 2015 included
+ 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 patches since version 2.9 was released, see the
+ <a href="releases.html#Jalview.2.9.0b2">Jalview 2.9.0b2 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>
- <p>
- <strong>Issues Resolved (a select list - see the <a
- href="releases.html#Jalview2.7">release history</a> for full details)
- </strong>
- </p>
- <p>
- <strong>Issues in the Jalview Desktop</strong>
- <ul>
- <li>Problems viewing associated structures for sequences
- retrieved from UNIPROT</li>
- <li>Problems viewing Jalview projects from older versions in
- version 2.6</li>
- <li>Preservation of hidden annotation rows and tree bootstrap
- values in projects</li>
- <li>Newly added JABAWS servers not always visible in web services
- menu</li>
- </ul>
- <strong>Issues specific to the JalviewLite Applet</strong>
- <ul>
- <li>Layout problems when lots of annotation rows are displayed</li>
- <li><= shown as = in annotation row tooltip</li>
- <li>export features raises exception when no features exist</li>
- <li>relative URLs not handled properly when used in parameters
- and annotation files</li>
- </ul>
- <strong>Issues affecting both applet and application</strong>
- <ul>
- <li>sequence numbering not preserved in MSF alignment output</li>
- <li>sequence associated secondary structure not correctly parsed
- in interleaved stockholm</li>
- <li>sequences containing lowercase letters are not properly
- associated with their pdb files</li>
- <li>Jalview PDB file reader does not extract sequence from deoxy
- nucleotide chains correctly</li>
- <li>Sequence length given in alignment properties window is off
- by 1</li>
- </ul>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff