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-
-What's new ?
-
-What's new ?
-Jalview Version 2.08
-Editing can be locked to the
- selection area so that any edits made within the locked area do
- not unexpectedly shift other parts of the alignment.
- Keyboard editing - press F2 to toggle cursor mode On / Off. For a full list
- of keyboard controls, look here.
- Create sequence features from searches.
- Previously, the regions of sequences highlighted as the result of
- searches were added as new regions in the alignment. Now, the sequence region
- selected by a search can be used to define named sequences features
- attached to the sequence, rather than the alignment.
-
-Sequence feature display and rendering has also been enhanced, with
- the addition of sequence feature groups (which can be used to show
- or hide a set of features en masse) and user defined
- feature colours as well as transparency controls, using the Sequence Feature Settings
- window. The Features file
- has also been extended to accomodate these enhancements.
-Alignment annotation and colouring is also considerably
- enhanced. Precalculated symbolic and quantitative annotations (text labels,
- secondary structure symbols and multiple scalar graphs) can now be
- loaded onto alignments via the Annotation
- File. Additionally, the Annotation
- Colouring dialog box allows an alignment to be coloured based on
- any of the graphed quantities with which it is annotated.
-Rendering speed has been improved by disabling anti-aliasing via
- the Smooth Fonts
- option in the View
- menu (its default set in Preferences). In addition, response
- times when editing alignments can be reduced by turning off the automatic
- calculation of amino acid property Consensus (which has been
- reintroduced to the Calculate menu as Autocalculate Consensus).
-
-Issues Resolved
-
-- Drag & Drop now works on common Linux desktops (at least KDE
-and Gnome)
-- Jalview XML Archive Input/Output is now faster (using an
-internal Jalview schema), and sequence description strings are now
-preserved in the archive.
-- Jalview can now correctly read and write MODELLER style
-PIR description lines for proteins with a PDB reference.
-
-
-See the Release History page for details of all
- new features and resolved issues.
-
-
+
+
+
+What's new ?
+
+
+
+ Jalview 2.10.2b1 bugfix release
+
+
+ This is patch release for 2.10.2. See the release notes for full
+ details about the bugs addressed. This release also introduces
+ additional improvements to the overview panel, and patches for
+ several minor issues including the ability to correctly recover
+ cross-references for Uniprot protein sequences from Ensembl.
+
+
+ What's new in Jalview 2.10.2 ?
+
+
+ Version 2.10.2 was released in August 2017, and introduced 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 2.10.2 Release Notes, but
+ the highlights are below.
+
+
+ - New dialog and faster and more
+ configurable Tree and PCA calculations
Menu entries for
+ calculating PCA and different types of tree have been replaced by
+ a single Calculations
+ dialog box. The underlying implementation for the PCA and tree
+ calculations have been made faster and more memory efficient.
+ - Extensible score models
A new
+ framework has also been created for the score models used to
+ calculate distances between sequences and shade alignments. This
+ framework allows import of substitution matrices in NCBI and
+ AAIndex format.
PCA Bug Fixes. Jalview's
+ implementation of PCA differed in its treatment of gaps and
+ non-standard residues. The BLOSUM62 matrix also included a typo
+ that affected results. See the 2.10.2 release note
+ about score model bugs for details and how to reinstate legacy
+ behaviour.
+ - Update to JABAWS 2.2
Jalview's
+ alignment, protein conservation analysis, and protein disorder and
+ RNA secondary structure prediction services are now provided by JABAWS 2.2.
+ Several of the programs provided as JABAWS 2.2 services have been
+ updated, so their options and parameters have changed.
+ - URL linkouts to other bioinformatics
+ databases
New preferences for opening web pages for
+ database cross-references via the UK Elixir's EMBL-EBI's MIRIAM
+ database and identifiers.org services.
+ - Showing and hiding regions
Hide insertions in the
+ PopUp menu has changed its behaviour. Prior to 2.10.2, columns
+ were only shown or hidden according to gaps in the sequence under
+ the popup menu. Now, only columns that are gapped in all selected
+ sequences as well as the sequence under the popup menu are hidden,
+ and column visibility outside the selected region is left as is.
+ This makes it easy to filter insertions from the alignment view
+ (just select the region containing insertions to remove) without
+ affecting the rest of the hidden columns.
+ - Gap count - a.k.a. the Occupancy
+ Annotation Row
Another way to filter columns according to
+ the presence of gaps is to enable the Occupancy
+ Annotation row via Jalview's Preferences. This annotation row
+ shows a histogram of the number of aligned residues at each
+ column. The Select
+ By Annotation dialog now also includes a percentage threshold
+ mode, to make it easy to filter alignments to show only those
+ columns with a particular fraction of aligned sequences.
+ - Recent search history for Find, PDBe and
+ Uniprot
Easily repeat a previous search for Find and the free
+ text search system (for querying Uniprot and the PDBe).
+ - Improved Overview Window
The alignment overview is now easier
+ to use when working with alignments of more than 5000 rows and
+ columns, and features a new pop-up menu that allows hidden regions
+ to be excluded from the overview. It also works with CDS/Protein
+ alignments and MSA views in wrapped mode.
+ - 3D Structure
Jalview's communication
+ with UCSF Chimera has been made more robust, particularly when
+ working with many structures and long sequences. Regions in
+ structures that correspond to hidden regions in an alignment view
+ are now left un-coloured, making it easier to highlight specific
+ features in 3D. See below for experimental
+ features for exchanging annotation between Chimera and Jalview.
+
+
+ Scripting
New groovy examples
+ demonstrate Jalview 2.10.2 APIs for creation of data-driven
+ colourschemes, and custom alignment file handlers. The FeatureAnnotationWorker
+ introduced in Jalview 2.10 has also been refactored to allow
+ efficient counting across multiple feature types. Please be aware
+ that feature counter scripts created for earlier versions will not
+ execute in Jalview 2.10.2.
+
+
+ Experimental Features
+
+
+ This release of Jalview introduces an Experimental Features
+ option in the Jalview Desktop's Tools menu that allows you
+ to try out features that are still in development. To access the
+ experimental features below - first enable the Tools→Enable
+ Experimental Features option, and then restart Jalview.
+
+
+
+
+