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
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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 2.10.2b2 bugfix release</strong>
30 This is patch release for 2.10.2. See the
31 <a href="releases.html#Jalview.2.10.2b2">release notes</a> for full
32 details about the bugs addressed. This second patch release fixes
33 problems with the Uniprot sequence fetcher and introduces secure SSL
34 connections for access to EMBL-EBI resources. The previous patch
35 release introduced additional improvements to the overview panel,
36 and patches for several minor issues including the ability to
37 correctly recover cross-references for Uniprot protein sequences
41 <strong>What's new in Jalview 2.10.2 ?</strong>
44 Version 2.10.2 was released in August 2017, and introduced new user
45 interface features, improved and more extensible tree and PCA
46 analysis, more robust 3D structure viewing with UCSF Chimera and an
47 updated service client for JABAWS. The full list of bug fixes and
48 new features can be found in the <a
49 href="releases.html#Jalview.2.10.2"> 2.10.2 Release Notes</a>, but
50 the highlights are below.
53 <li><strong>New dialog and faster and more
54 configurable Tree and PCA calculations</strong><br> Menu entries for
55 calculating PCA and different types of tree have been replaced by
56 a single <a href="calculations/calculations.html"><em>Calculations</em>
57 dialog box</a>. The underlying implementation for the PCA and tree
58 calculations have been made faster and more memory efficient.</li>
59 <li><strong>Extensible score models</strong><br />A new
60 framework has also been created for the score models used to
61 calculate distances between sequences and shade alignments. This
62 framework allows import of substitution matrices in NCBI and
63 AAIndex format.<br /> <strong>PCA Bug Fixes</strong>. Jalview's
64 implementation of PCA differed in its treatment of gaps and
65 non-standard residues. The BLOSUM62 matrix also included a typo
66 that affected results. See the <a
67 href="releases.html#2102scoremodelbugs">2.10.2 release note
68 about score model bugs</a> for details and how to reinstate legacy
70 <li><strong>Update to JABAWS 2.2</strong><br />Jalview's
71 alignment, protein conservation analysis, and protein disorder and
72 RNA secondary structure prediction services are now provided by <a
73 href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS 2.2</a>.
74 Several of the programs provided as JABAWS 2.2 services have been
75 updated, so their options and parameters have changed.</li>
76 <li><strong>URL linkouts to other bioinformatics
77 databases</strong><br />New preferences for <a
78 href="webServices/urllinks.html">opening web pages for
79 database cross-references</a> via the UK Elixir's EMBL-EBI's MIRIAM
80 database and identifiers.org services.</li>
81 <li><strong>Showing and hiding regions</strong> <br /> <a
82 href="menus/popupMenu.html#hideinserts">Hide insertions</a> in the
83 PopUp menu has changed its behaviour. Prior to 2.10.2, columns
84 were only shown or hidden according to gaps in the sequence under
85 the popup menu. Now, only columns that are gapped in all selected
86 sequences as well as the sequence under the popup menu are hidden,
87 and column visibility outside the selected region is left as is.
88 This makes it easy to filter insertions from the alignment view
89 (just select the region containing insertions to remove) without
90 affecting the rest of the hidden columns.</li>
91 <li><strong>Gap count - a.k.a. the Occupancy
92 Annotation Row</strong><br /> Another way to filter columns according to
93 the presence of gaps is to enable the <strong>Occupancy
94 Annotation</strong> row via Jalview's Preferences. This annotation row
95 shows a histogram of the number of aligned residues at each
96 column. The <a href="features/columnFilterByAnnotation.html">Select
97 By Annotation</a> dialog now also includes a percentage threshold
98 mode, to make it easy to filter alignments to show only those
99 columns with a particular fraction of aligned sequences.</li>
100 <li><strong>Recent search history for Find, PDBe and
101 Uniprot</strong><br />Easily repeat a previous search for <a
102 href="features/search.html#queryhistory">Find</a> and the free
103 text search system (for querying Uniprot and the PDBe).</li>
104 <li><strong>Improved Overview Window</strong><br />The <a
105 href="features/overview.html">alignment overview</a> is now easier
106 to use when working with alignments of more than 5000 rows and
107 columns, and features a new pop-up menu that allows hidden regions
108 to be excluded from the overview. It also works with CDS/Protein
109 alignments and MSA views in wrapped mode.</li>
110 <li><strong>3D Structure</strong><br />Jalview's communication
111 with UCSF Chimera has been made more robust, particularly when
112 working with many structures and long sequences. Regions in
113 structures that correspond to hidden regions in an alignment view
114 are now left un-coloured, making it easier to highlight specific
115 features in 3D. See below for <a href="#experimental">experimental
116 features for exchanging annotation between Chimera and Jalview.</a></li>
119 <strong>Scripting</strong><br />New <a
120 href="http://www.jalview.org/examples/groovy">groovy examples</a>
121 demonstrate Jalview 2.10.2 APIs for creation of data-driven
122 colourschemes, and custom alignment file handlers. The <a
123 href="groovy/featuresCounter.html">FeatureAnnotationWorker</a>
124 introduced in Jalview 2.10 has also been refactored to allow
125 efficient counting across multiple feature types. Please be aware
126 that feature counter scripts created for earlier versions will not
127 execute in Jalview 2.10.2.
130 <strong><a name="experimental">Experimental Features</a></strong>
133 This release of Jalview introduces an <em>Experimental Features</em>
134 option in the Jalview Desktop's <em>Tools</em> menu that allows you
135 to try out features that are still in development. To access the
136 experimental features below - first enable the <strong>Tools→Enable
137 Experimental Features</strong> option, and then restart Jalview.
140 <li><em>Annotation transfer between Chimera and Jalview</em><br />Two
141 <a href="features/chimera.html#experimental">new entries in
142 the Chimera viewer's Chimera menu</a> allow positional annotation to
143 be exchanged between Chimera and Jalview.</li>