<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>What's new ?</title>
</head>
<body>
-<p><strong>What's new ?</strong></p>
+ <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>
-<p><strong>Jalview Version 2.2</strong></p>
-<p>Multiple views with different styles, colours, hidden regions for
-one alignment</p>
-<p>Easily add, amend and delete sequence features</p>
-<p>"Reload" alignment from File or URL to revert to
-original</p>
-<p>"Save" to current filename or "Save As" to
-new filename</p>
-<p>New <strong>"New Window"</strong> button on the
-"Output To Textbox" opens output window for quick 'sequence
-editing'.</p>
-<p>Set different text colour for dark or light background</p>
-<p>Right align sequence ids</p>
-<p>Set colour of lower case residues in a user defined colour scheme
-</p>
-<p>Menu Rearrangements: New <strong>Format</strong> for alignment
-layout and <strong>Select</strong> for region selection.</p>
-</p>
-<p>Menu item accelerator keys added</p>
-<p>Control-V pastes sequences to active window, Control-Shift-V
-pastes to a new window.</p>
-<p>Raise/Minimise alignment and all associated windows from desktop
-window's <strong>window</strong> menu</p>
-<p>Select and colour whole branches of a tree</p>
-<p>'New Window' button on the 'Output to Text box' alignment output
-option to open a new alignment window after editing.</p>
-<p><strong>Issues Resolved</strong></p>
-</p>
-<p>Optimisations for large alignments: faster multithreaded
-calculations and Undo/Redo system.</p>
-<p>Remove empty columns - if empty columns exist at the end of the
-alignment bug fixed.</p>
-<p>DAS feature fetching slowed down, doesn't overload DAS servers</p>
-<p>DAS feature fetching can be cancelled</p>
-<p>Correct display of > and < symbols for feature descriptions
-without explicit <html> tags.</p>
-<p>Zoom working in PCA viewer</p>
-<p>Sequence Descriptions retained after running a web service</p>
-<p> </p>
-<p>See the <a href="releases.html">Release History</a> page for
-details of all new features and resolved issues.</p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff