3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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16 * PURPOSE. See the GNU General Public License for more details.
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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>
29 <p>This August 2018 release of Jalview introduces new user interface features, improved and more extensible tree and PCA analysis, more robust 3D structure viewing with UCSF Chimera and an updated service client for JABAWS. The full list of bug fixes and new features can be found in the <a
30 href="releases.html#Jalview.2.10.2"> 2.10.2 Release Notes</a>, but the
34 <li><strong>New dialog and faster and more
35 configurable Tree and PCA calculations</strong><br> Menu entries for
36 calculating PCA and different types of tree have been replaced by
37 a single <a href="calculations/calculations.html"><em>Calculations</em>
38 dialog box</a>. The underlying implementation for the PCA and tree
39 calculations have been made faster and more memory efficient.</li>
40 <li><strong>Extensible score models</strong><br />A new
41 framework has also been created for the score models used to
42 calculate distances between sequences and shade alignments. This
43 framework allows import of substitution matrices in NCBI and
45 <strong>PCA Bug Fixes</strong>. Jalview's implementation of PCA
46 differed in its treatment of gaps and non-standard residues. The
47 BLOSUM62 matrix also included a typo that affected results. See the
48 <a href="releases.html#2102scoremodelbugs">2.10.2 release note
49 about score model bugs</a> for details and how to reinstate legacy
51 <li><strong>Update to JABAWS 2.2</strong><br />Jalview's
52 alignment, protein conservation analysis, and protein disorder and
53 RNA secondary structure prediction services are now provided by <a
54 href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS 2.2</a>.
55 Several of the programs provided as JABAWS 2.2 services have been
56 updated, so their options and parameters have changed.</li>
57 <li><strong>URL linkouts to other bioinformatics
58 databases</strong><br />New preferences for <a
59 href="webServices/urllinks.html">opening web pages for
60 database cross-references</a> via the UK Elixir's EMBL-EBI's MIRIAM
61 database and identifiers.org services.</li>
62 <li><strong>Showing and hiding regions</strong> <br /> <a
63 href="menus/popupMenu.html#hideinserts">Hide insertions</a> in the
64 PopUp menu has changed its behaviour. Prior to 2.10.2, columns
65 were only shown or hidden according to gaps in the sequence under
66 the popup menu. Now, only columns that are gapped in all selected
67 sequences as well as the sequence under the popup menu are hidden,
68 and column visibility outside the selected region is left as is.
69 This makes it easy to filter insertions from the alignment view
70 (just select the region containing insertions to remove) without
71 affecting the rest of the hidden columns.</li>
72 <li><strong>Gap count - a.k.a. the Occupancy
73 Annotation Row</strong><br /> Another way to filter columns according to
74 the presence of gaps is to enable the <strong>Occupancy
75 Annotation</strong> row via Jalview's Preferences. This annotation row
76 shows a histogram of the number of aligned residues at each
77 column. The <a href="features/columnFilterByAnnotation.html">Select
78 By Annotation</a> dialog now also includes a percentage threshold
79 mode, to make it easy to filter alignments to show only those
80 columns with a particular fraction of aligned sequences.</li>
81 <li><strong>Recent search history for Find, PDBe and
82 Uniprot</strong><br />Easily repeat a previous search for <a
83 href="features/search.html#queryhistory">Find</a> and the free
84 text search system (for querying Uniprot and the PDBe).</li>
85 <li><strong>Improved Overview Window</strong><br />The <a
86 href="features/overview.html">alignment overview</a> is now easier
87 to use when working with alignments of more than 5000 rows and
88 columns, and features a new pop-up menu that allows hidden regions
89 to be excluded from the overview. It also works with CDS/Protein
90 alignments and MSA views in wrapped mode.</li>
91 <li><strong>3D Structure</strong><br />Jalview's communication
92 with UCSF Chimera has been made more robust, particularly when
93 working with many structures and long sequences. Regions in
94 structures that correspond to hidden regions in an alignment view
95 are now left un-coloured, making it easier to highlight specific
96 features in 3D. See below for <a href="#experimental">experimental
97 features for exchanging annotation between Chimera and Jalview.</a></li>
100 <strong>Scripting</strong><br />New <a
101 href="http://www.jalview.org/examples/groovy">groovy examples</a>
102 demonstrate Jalview 2.10.2 APIs for creation of data-driven
103 colourschemes, and custom alignment file handlers. The <a
104 href="groovy/featuresCounter.html">FeatureAnnotationWorker</a>
105 introduced in Jalview 2.10 has also been refactored to allow
106 efficient counting across multiple feature types. Please be aware
107 that feature counter scripts created for earlier versions will not
108 execute in Jalview 2.10.2.
111 <strong><a name="experimental">Experimental Features</a></strong>
114 This release of Jalview introduces an <em>Experimental Features</em>
115 option in the Jalview Desktop's <em>Tools</em> menu that allows you
116 to try out features that are still in development. To access the
117 experimental features below - first enable the <strong>Tools→Enable
118 Experimental Features</strong> option, and then restart Jalview.
121 <li><em>Annotation transfer between Chimera and Jalview</em><br />Two
122 <a href="features/chimera.html#experimental">new entries in
123 the Chimera viewer's Chimera menu</a> allow positional annotation to
124 be exchanged between Chimera and Jalview.</li>