-<html>\r
-<head>\r
-<title>What's new ?</title>\r
-</head>\r
-<body>\r
-<p><strong>What's new ?</strong></p>\r
-\r
-<p><strong>Jalview Version 2.2.1</strong></p>\r
-<p>Non standard characters can be read and displayed </p>\r
-<p>Annotations/Features can be imported/exported to the applet via textbox </p>\r
-<p>Applet allows editing of sequence/annotation/group name & description </p>\r
-<p>Preference setting to display sequence name in italics </p>\r
-<p>Annotation file format extended to allow Sequence_groups to be defined</p>\r
-<p> </p>\r
-<p><strong>Issues Resolved</strong></p>\r
-<p><br>\r
- Applet crash under certain Linux OS with Java 1.6 installed </p>\r
-<p>Annotation file export / import bugs fixed </p>\r
-<p>PNG / EPS image output bugs fixed<br>\r
-</p>\r
-<p> </p>\r
-<p>See the <a href="releases.html">Release History</a> page for\r
-details of all new features and resolved issues.</p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 in Jalview 2.10.2 ?</strong>
+ </p>
+ <p>
+ Full details about Jalview 2.10.2 are in the <a
+ href="releases.html#Jalview.2.10.2"> Release Notes</a>, but the
+ highlights are below.
+ </p>
+ <ul>
+ <li><strong>New UI, and faster and more configurable implementation for PCA, Neighbour-Joining and UPGMA Trees</strong><br>
+ Menu entries for calculating PCA and different types of tree have
+ been replaced by a single <em>Calculations</em> dialog box. The
+ underlying implementation for the PCA and tree calculations have been
+ made faster and more memory efficient. A new framework has also been
+ created for the score models used to calculate distances between
+ sequences. This framework allows import of substitution matrices in
+ NCBI and AAIndex format, and custom score models to be created via a
+ groovy script.</li>
+ <li><strong>Update to JABAWS 2.2</strong><br />Jalview's
+ alignment, protein conservation analysis, and protein disorder and
+ RNA secondary structure prediction services are now provided by <a
+ href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS 2.2</a>.
+ Several of the programs provided as services have been updated, so
+ their options and parameters have changed.</li>
+ <li>New preferences for <a href="webServices/urllinks.html">opening
+ web pages for database cross-references</a> via the UK Elixir's
+ EMBL-EBI's MIRIAM database and identifiers.org services.
+ </li>
+ <li><em>Showing and hiding regions</em>
+ <ul>
+ <li><a href="menus/popupMenu.html#hideinserts">Hide
+ insertions</a> in the PopUp menu has changed its behaviour.
+ Prior to 2.10.2, columns were only shown or hidden according
+ to gaps in the sequence under the popup menu. Now, only
+ columns that are gapped in all selected sequences as well as
+ the sequence under the popup menu are hidden, and column
+ visibility outside the selected region is left as is. This
+ makes it easy to filter insertions from the alignment view
+ (just select the region containing insertions to remove)
+ without affecting the rest of the hidden columns.</li>
+ </ul></li>
+ </ul>
+ <p>
+ <strong><a name="experimental">Experimental Features</a></strong>
+ </p>
+ <p>
+ This release of Jalview includes a new option in the Jalview Desktop
+ that allows you to try out features that are still in development.
+ To access the features described below, please first enable the <strong>Tools→Enable
+ Experimental Features</strong> option, and then restart Jalview.
+ </p>
+ <ul>
+ <li><em>Annotation transfer between Chimera and Jalview</em><br />Two
+ <a href="features/chimera.html#experimental">new entries in
+ the Chimera viewer's Chimera menu</a> allow positional annotation to
+ be exchanged between Chimera and Jalview.</li>
+ </ul>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff