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 This August 2017 release of Jalview introduces new user interface
31 features, improved and more extensible tree and PCA analysis, more
32 robust 3D structure viewing with UCSF Chimera and an updated service
33 client for JABAWS. The full list of bug fixes and new features can
34 be found in the <a href="releases.html#Jalview.2.10.2"> 2.10.2
35 Release Notes</a>, but the highlights are below.
38 <li><strong>New dialog and faster and more
39 configurable Tree and PCA calculations</strong><br> Menu entries for
40 calculating PCA and different types of tree have been replaced by
41 a single <a href="calculations/calculations.html"><em>Calculations</em>
42 dialog box</a>. The underlying implementation for the PCA and tree
43 calculations have been made faster and more memory efficient.</li>
44 <li><strong>Extensible score models</strong><br />A new
45 framework has also been created for the score models used to
46 calculate distances between sequences and shade alignments. This
47 framework allows import of substitution matrices in NCBI and
48 AAIndex format.<br /> <strong>PCA Bug Fixes</strong>. Jalview's
49 implementation of PCA differed in its treatment of gaps and
50 non-standard residues. The BLOSUM62 matrix also included a typo
51 that affected results. See the <a
52 href="releases.html#2102scoremodelbugs">2.10.2 release note
53 about score model bugs</a> for details and how to reinstate legacy
55 <li><strong>Update to JABAWS 2.2</strong><br />Jalview's
56 alignment, protein conservation analysis, and protein disorder and
57 RNA secondary structure prediction services are now provided by <a
58 href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS 2.2</a>.
59 Several of the programs provided as JABAWS 2.2 services have been
60 updated, so their options and parameters have changed.</li>
61 <li><strong>URL linkouts to other bioinformatics
62 databases</strong><br />New preferences for <a
63 href="webServices/urllinks.html">opening web pages for
64 database cross-references</a> via the UK Elixir's EMBL-EBI's MIRIAM
65 database and identifiers.org services.</li>
66 <li><strong>Showing and hiding regions</strong> <br /> <a
67 href="menus/popupMenu.html#hideinserts">Hide insertions</a> in the
68 PopUp menu has changed its behaviour. Prior to 2.10.2, columns
69 were only shown or hidden according to gaps in the sequence under
70 the popup menu. Now, only columns that are gapped in all selected
71 sequences as well as the sequence under the popup menu are hidden,
72 and column visibility outside the selected region is left as is.
73 This makes it easy to filter insertions from the alignment view
74 (just select the region containing insertions to remove) without
75 affecting the rest of the hidden columns.</li>
76 <li><strong>Gap count - a.k.a. the Occupancy
77 Annotation Row</strong><br /> Another way to filter columns according to
78 the presence of gaps is to enable the <strong>Occupancy
79 Annotation</strong> row via Jalview's Preferences. This annotation row
80 shows a histogram of the number of aligned residues at each
81 column. The <a href="features/columnFilterByAnnotation.html">Select
82 By Annotation</a> dialog now also includes a percentage threshold
83 mode, to make it easy to filter alignments to show only those
84 columns with a particular fraction of aligned sequences.</li>
85 <li><strong>Recent search history for Find, PDBe and
86 Uniprot</strong><br />Easily repeat a previous search for <a
87 href="features/search.html#queryhistory">Find</a> and the free
88 text search system (for querying Uniprot and the PDBe).</li>
89 <li><strong>Improved Overview Window</strong><br />The <a
90 href="features/overview.html">alignment overview</a> is now easier
91 to use when working with alignments of more than 5000 rows and
92 columns, and features a new pop-up menu that allows hidden regions
93 to be excluded from the overview. It also works with CDS/Protein
94 alignments and MSA views in wrapped mode.</li>
95 <li><strong>3D Structure</strong><br />Jalview's communication
96 with UCSF Chimera has been made more robust, particularly when
97 working with many structures and long sequences. Regions in
98 structures that correspond to hidden regions in an alignment view
99 are now left un-coloured, making it easier to highlight specific
100 features in 3D. See below for <a href="#experimental">experimental
101 features for exchanging annotation between Chimera and Jalview.</a></li>
104 <strong>Scripting</strong><br />New <a
105 href="http://www.jalview.org/examples/groovy">groovy examples</a>
106 demonstrate Jalview 2.10.2 APIs for creation of data-driven
107 colourschemes, and custom alignment file handlers. The <a
108 href="groovy/featuresCounter.html">FeatureAnnotationWorker</a>
109 introduced in Jalview 2.10 has also been refactored to allow
110 efficient counting across multiple feature types. Please be aware
111 that feature counter scripts created for earlier versions will not
112 execute in Jalview 2.10.2.
115 <strong><a name="experimental">Experimental Features</a></strong>
118 This release of Jalview introduces an <em>Experimental Features</em>
119 option in the Jalview Desktop's <em>Tools</em> menu that allows you
120 to try out features that are still in development. To access the
121 experimental features below - first enable the <strong>Tools→Enable
122 Experimental Features</strong> option, and then restart Jalview.
125 <li><em>Annotation transfer between Chimera and Jalview</em><br />Two
126 <a href="features/chimera.html#experimental">new entries in
127 the Chimera viewer's Chimera menu</a> allow positional annotation to
128 be exchanged between Chimera and Jalview.</li>