3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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11 * of the License, or (at your option) any later version.
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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>Jalview 2.10.2b1 bugfix release</strong>
30 This is patch release for 2.10.2. See the <a
31 href="releases.html#Jalview.2.10.2b1">release notes</a>.
34 <strong>What's new in Jalview 2.10.2 ?</strong>
37 Version 2.10.2 was released in August 2017, and introduced new user
38 interface features, improved and more extensible tree and PCA
39 analysis, more robust 3D structure viewing with UCSF Chimera and an
40 updated service client for JABAWS. The full list of bug fixes and
41 new features can be found in the <a
42 href="releases.html#Jalview.2.10.2"> 2.10.2 Release Notes</a>, but
43 the highlights are below.
46 <li><strong>New dialog and faster and more
47 configurable Tree and PCA calculations</strong><br> Menu entries for
48 calculating PCA and different types of tree have been replaced by
49 a single <a href="calculations/calculations.html"><em>Calculations</em>
50 dialog box</a>. The underlying implementation for the PCA and tree
51 calculations have been made faster and more memory efficient.</li>
52 <li><strong>Extensible score models</strong><br />A new
53 framework has also been created for the score models used to
54 calculate distances between sequences and shade alignments. This
55 framework allows import of substitution matrices in NCBI and
56 AAIndex format.<br /> <strong>PCA Bug Fixes</strong>. Jalview's
57 implementation of PCA differed in its treatment of gaps and
58 non-standard residues. The BLOSUM62 matrix also included a typo
59 that affected results. See the <a
60 href="releases.html#2102scoremodelbugs">2.10.2 release note
61 about score model bugs</a> for details and how to reinstate legacy
63 <li><strong>Update to JABAWS 2.2</strong><br />Jalview's
64 alignment, protein conservation analysis, and protein disorder and
65 RNA secondary structure prediction services are now provided by <a
66 href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS 2.2</a>.
67 Several of the programs provided as JABAWS 2.2 services have been
68 updated, so their options and parameters have changed.</li>
69 <li><strong>URL linkouts to other bioinformatics
70 databases</strong><br />New preferences for <a
71 href="webServices/urllinks.html">opening web pages for
72 database cross-references</a> via the UK Elixir's EMBL-EBI's MIRIAM
73 database and identifiers.org services.</li>
74 <li><strong>Showing and hiding regions</strong> <br /> <a
75 href="menus/popupMenu.html#hideinserts">Hide insertions</a> in the
76 PopUp menu has changed its behaviour. Prior to 2.10.2, columns
77 were only shown or hidden according to gaps in the sequence under
78 the popup menu. Now, only columns that are gapped in all selected
79 sequences as well as the sequence under the popup menu are hidden,
80 and column visibility outside the selected region is left as is.
81 This makes it easy to filter insertions from the alignment view
82 (just select the region containing insertions to remove) without
83 affecting the rest of the hidden columns.</li>
84 <li><strong>Gap count - a.k.a. the Occupancy
85 Annotation Row</strong><br /> Another way to filter columns according to
86 the presence of gaps is to enable the <strong>Occupancy
87 Annotation</strong> row via Jalview's Preferences. This annotation row
88 shows a histogram of the number of aligned residues at each
89 column. The <a href="features/columnFilterByAnnotation.html">Select
90 By Annotation</a> dialog now also includes a percentage threshold
91 mode, to make it easy to filter alignments to show only those
92 columns with a particular fraction of aligned sequences.</li>
93 <li><strong>Recent search history for Find, PDBe and
94 Uniprot</strong><br />Easily repeat a previous search for <a
95 href="features/search.html#queryhistory">Find</a> and the free
96 text search system (for querying Uniprot and the PDBe).</li>
97 <li><strong>Improved Overview Window</strong><br />The <a
98 href="features/overview.html">alignment overview</a> is now easier
99 to use when working with alignments of more than 5000 rows and
100 columns, and features a new pop-up menu that allows hidden regions
101 to be excluded from the overview. It also works with CDS/Protein
102 alignments and MSA views in wrapped mode.</li>
103 <li><strong>3D Structure</strong><br />Jalview's communication
104 with UCSF Chimera has been made more robust, particularly when
105 working with many structures and long sequences. Regions in
106 structures that correspond to hidden regions in an alignment view
107 are now left un-coloured, making it easier to highlight specific
108 features in 3D. See below for <a href="#experimental">experimental
109 features for exchanging annotation between Chimera and Jalview.</a></li>
112 <strong>Scripting</strong><br />New <a
113 href="http://www.jalview.org/examples/groovy">groovy examples</a>
114 demonstrate Jalview 2.10.2 APIs for creation of data-driven
115 colourschemes, and custom alignment file handlers. The <a
116 href="groovy/featuresCounter.html">FeatureAnnotationWorker</a>
117 introduced in Jalview 2.10 has also been refactored to allow
118 efficient counting across multiple feature types. Please be aware
119 that feature counter scripts created for earlier versions will not
120 execute in Jalview 2.10.2.
123 <strong><a name="experimental">Experimental Features</a></strong>
126 This release of Jalview introduces an <em>Experimental Features</em>
127 option in the Jalview Desktop's <em>Tools</em> menu that allows you
128 to try out features that are still in development. To access the
129 experimental features below - first enable the <strong>Tools→Enable
130 Experimental Features</strong> option, and then restart Jalview.
133 <li><em>Annotation transfer between Chimera and Jalview</em><br />Two
134 <a href="features/chimera.html#experimental">new entries in
135 the Chimera viewer's Chimera menu</a> allow positional annotation to
136 be exchanged between Chimera and Jalview.</li>