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.
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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
36 implementation for PCA, Neighbour-Joining and UPGMA Trees</strong><br>
37 Menu entries for calculating PCA and different types of tree have
38 been replaced by a single <em>Calculations</em> dialog box. The
39 underlying implementation for the PCA and tree calculations have
40 been made faster and more memory efficient. A new framework has
41 also been created for the score models used to calculate distances
42 between sequences. This framework allows import of substitution
43 matrices in NCBI and AAIndex format, and custom score models to be
44 created via a groovy script.</li>
45 <li><strong>Update to JABAWS 2.2</strong><br />Jalview's
46 alignment, protein conservation analysis, and protein disorder and
47 RNA secondary structure prediction services are now provided by <a
48 href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS 2.2</a>.
49 Several of the programs provided as services have been updated, so
50 their options and parameters have changed.</li>
51 <li>New preferences for <a href="webServices/urllinks.html">opening
52 web pages for database cross-references</a> via the UK Elixir's
53 EMBL-EBI's MIRIAM database and identifiers.org services.
55 <li><em>Showing and hiding regions</em>
57 <li><a href="menus/popupMenu.html#hideinserts">Hide
58 insertions</a> in the PopUp menu has changed its behaviour.
59 Prior to 2.10.2, columns were only shown or hidden according
60 to gaps in the sequence under the popup menu. Now, only
61 columns that are gapped in all selected sequences as well as
62 the sequence under the popup menu are hidden, and column
63 visibility outside the selected region is left as is. This
64 makes it easy to filter insertions from the alignment view
65 (just select the region containing insertions to remove)
66 without affecting the rest of the hidden columns.</li>
68 <li>Recent search histories for <a
69 href="features/search.html#queryhistory">Find</a> and the free
70 text search system (for querying Uniprot and the PDBe).</li>
73 <strong><a name="experimental">Experimental Features</a></strong>
76 This release of Jalview includes a new option in the Jalview Desktop
77 that allows you to try out features that are still in development.
78 To access the features described below, please first enable the <strong>Tools→Enable
79 Experimental Features</strong> option, and then restart Jalview.
82 <li><em>Annotation transfer between Chimera and Jalview</em><br />Two
83 <a href="features/chimera.html#experimental">new entries in
84 the Chimera viewer's Chimera menu</a> allow positional annotation to
85 be exchanged between Chimera and Jalview.</li>
88 <strong>Scripting</strong><br />New <a
89 href="http://www.jalview.org/examples/groovy">groovy examples</a>
90 demonstrate Jalview 2.10.2 APIs for creation of data-driven
91 colourschemes, and custom alignment file handlers. The <a
92 href="groovy/featuresCounter.html">FeatureAnnotationWorker</a>
93 introduced in Jalview 2.10 has also been refactored to allow
94 efficient counting across multiple feature types. Please be aware
95 that feature counter scripts created for earlier versions will not
96 execute in Jalview 2.10.2.