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 2.11.1.0</strong>
30 Jalview 2.11.1.0 is the first minor release for the 2.11 series.
31 Along with a number of critical bug fixes and improvements it brings
32 new functionality for mapping sequence features between CDS and
33 Protein alignments. It is also the first release made under a new <em>four</em>
34 number versioning scheme, which will allow us to keep track of
35 patches and bug fixes.
38 <li><strong>Virtual Features</strong><br />In previous
39 versions of Jalview, specific nucleotide sequence features such as
40 genomic variants and exons were transferred to protein products on
41 import. Jalview 2.11.1 instead provides 'virtual features' that
42 can be enabled and overlaid on linked CDS/Protein views via their
43 <a href="features/splitView.html#virtualfeats">Sequence
44 Features dialog</a>. This allows more analyses of nucleotide and
45 peptide sequence features on alignments in a more flexible and
46 memory efficient way than in earlier versions.</li>
47 <li><strong>Improved VCF data import</strong><br /> <a
48 href="features/importvcf.html#attribs">Standard attributes for
49 filtering variants</a> (e.g. position, QUAL field etc) are now
50 extracted from VCF files. This new feature was suggested by a user
51 at the Jalview booth during ISMB 2019.</li>
52 <li><strong>Extended feature attributes are exported
53 in GFF3</strong><br />Complex attributes from VCF files can be exported
54 and imported via GFF3</li>
55 <li><strong>Updated Jalview Installer and Launcher</strong><br />Jalview's
56 installation packages are now built with Install4j 8, which brings
57 better support for Linux and improved control of file
58 associations. New <a href="memory.html#jvm">parameters on the
59 Jalview launcher</a> allow an upper memory limit to be specified <em>via</em>
60 a Jalview launch file, to prevent it from hogging your system.</li>
63 See the <a href="releases.html#Jalview.2.11.1.0">2.11.1.0
64 release notes</a> for full details of bugs fixed and new known issues.
67 <em>JalviewJS News</em><br />With the release of Jalview 2.11.1.0,
68 the team are now focused on bringing JalviewJS to full production.
69 To follow our progress take a look at <em>http://www.jalview.org/jalview-js/</em>
70 and follow updates on our new <a
71 href="https://github.com/jalview/jalview-js/">JalviewJS
72 Releases github repository</a>.