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>What's new in Jalview 2.10.2 ?</strong>
30 Full details about Jalview 2.10.2 are in the <a
31 href="releases.html#Jalview.2.10.2"> Release Notes</a>, but the
35 <li><strong>New UI, and faster and more configurable implementation for PCA, Neighbour-Joining and UPGMA Trees</strong><br>
36 Menu entries for calculating PCA and different types of tree have
37 been replaced by a single <em>Calculations</em> dialog box. The
38 underlying implementation for the PCA and tree calculations have been
39 made faster and more memory efficient. A new framework has also been
40 created for the score models used to calculate distances between
41 sequences. This framework allows import of substitution matrices in
42 NCBI and AAIndex format, and custom score models to be created via a
44 <li><strong>Update to JABAWS 2.2</strong><br />Jalview's
45 alignment, protein conservation analysis, and protein disorder and
46 RNA secondary structure prediction services are now provided by <a
47 href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS 2.2</a>.
48 Several of the programs provided as services have been updated, so
49 their options and parameters have changed.</li>
50 <li>New preferences for <a href="webServices/urllinks.html">opening
51 web pages for database cross-references</a> via the UK Elixir's
52 EMBL-EBI's MIRIAM database and identifiers.org services.
54 <li><em>Showing and hiding regions</em>
56 <li><a href="menus/popupMenu.html#hideinserts">Hide
57 insertions</a> in the PopUp menu has changed its behaviour.
58 Prior to 2.10.2, columns were only shown or hidden according
59 to gaps in the sequence under the popup menu. Now, only
60 columns that are gapped in all selected sequences as well as
61 the sequence under the popup menu are hidden, and column
62 visibility outside the selected region is left as is. This
63 makes it easy to filter insertions from the alignment view
64 (just select the region containing insertions to remove)
65 without affecting the rest of the hidden columns.</li>
69 <strong><a name="experimental">Experimental Features</a></strong>
72 This release of Jalview includes a new option in the Jalview Desktop
73 that allows you to try out features that are still in development.
74 To access the features described below, please first enable the <strong>Tools→Enable
75 Experimental Features</strong> option, and then restart Jalview.
78 <li><em>Annotation transfer between Chimera and Jalview</em><br />Two
79 <a href="features/chimera.html#experimental">new entries in
80 the Chimera viewer's Chimera menu</a> allow positional annotation to
81 be exchanged between Chimera and Jalview.</li>