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What's new ?
-
- What's new ?
Jalview 2.8.0b1 is a bugfix
- release for Jalview version 2.8.
As usual you can find the
- highlights below, and the comprehensive list is given in the Jalview 2.8.0b1 Release Notes.
-
- This bug fix release includes numerous minor enhancements made over
- the last 12 months. Importantly, it is also the first release that
- provides Jalview as a trusted application, signed with a certificate
- donated to us by Certum.
+ Jalview 2.10.2b1 bugfix release
- Enhancements and new features
-
- - Allow disorder predictions to be made on the current
- selection (or visible selection) in the same way that JPred works
- - allow import of data from gzipped files
- - Improved per-sequence 'colour-by-annotation' performance
- - Support '' style escaping of quotes in Newick files
- - group options for JABAWS service by command line name
- - Select primary source when selecting authority in database
- fetcher GUI
- - COMBINE statement uses current SEQUENCE_REF and GROUP_REF
- scope to group annotation rows
- - add .mfa to FASTA file extensions recognised by Jalview
- - groovy scripting for headless jalview operation
- - Output in Stockholm format
-
- Bug fixes
-
- - Uniprot and PDB database cross-reference fetching works
- properly
- - 'View all structures' in the desktop is more reliable
- - Web services parameter dialog box shows the options enabled
- for different presets
- - Interactive creation of RNA secondary structure works more
- smoothly
- - Keyboard mode 'P' command jumps to the right place
- - Improved support for parsing database cross-references via
- Stockholm and Rfam database
- - Improved semantics in annotation files for grouping
- annotation rows associated with particular sequences and groups
- - More robust DNA->Amino acid translation
- - Improved Headless-mode operation for DAS annotation
- retrieval, groovy script execution and alignment figure generation
- - annotation label tooltip text needs to be wrapped
-
+
+ This is patch release for 2.10.2. See the release notes for full
+ details bugs addressed in this version, which 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.
+
+
+