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51 calculating PCA and different types of tree have been replaced by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