3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>What's new ?</title>
27 <strong>Jalview 2.11 - major and minor new features</strong>
29 <p>Jalview 2.11 introduces support for loading VCF files, and new
30 filters and shading models for sequence features. Under the hood,
31 we've addressed many bugs, and also made some important changes in
32 the way the Jalview desktop is installed and launched.</p>
34 <li><em>VCF Support</em>. Proteins and genomic contigs with
35 chromosomal location annotation (such as protein coding genes
36 retrieved from Ensembl) can be annotated with variants <a
37 href="features/importvcf.html">imported from a local VCF file</a>.</li>
38 <li><em>The Jalview Launcher and Update System</em><br />
39 Jalview's new installation model means you'll only need to
40 download and install Jalview once. After installation, Jalview
41 will automatically keep itself up to date. The launcher also sets
42 Jalview's memory automatically, so you'll never again have to
43 manually configure Java's memory settings.<br />We are grateful
44 to Install4J who provided us with a free license for their
45 installation system, and Jalview's over the air update system is
46 based on Three Rings' Getdown system.</li>
47 <li><em>Backup files</em><br />Jalview will automatically
48 create backups when overwriting existing files, and - unlike with
49 earlier versions, should Jalview crash during a save, the original
50 file will be unaffected.</li>
51 <li><em>PCA plots stored in Jalview Projects</em><br />The PCA
52 viewer has also been enhanced and the user interface revised.</li>
57 The full list of bugs fixed in this release can be found in the <a
58 href="releases.html#Jalview.2.11.0">2.11 Release Notes</a>.
61 <strong>Jalview and Java 11, 13, and onwards</strong>
63 <p>The Jalview application comes bundled with its own independent
64 Java installation which will be updated automatically from
65 www.jalview.org. Version 2.11.0 includes an AdoptOpenJDK Java 1.8
66 runtime, but installations will be migrated to the latest Java
67 release once remaining issues have been addressed.</p>