Jalview 2.10.2b1 bugfix release
This is patch release for 2.10.2. See the release notes.
- Gaps are now rendered as dark grey in overview window
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calculating PCA and different types of tree have been replaced by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.