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52 calculating PCA and different types of tree have been replaced by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