What's new in Jalview 2.10.2 ?
Full details about Jalview 2.10.2 are in the Release Notes, but the
highlights are below.
- New UI, and faster and more configurable
implementation for PCA, Neighbour-Joining and UPGMA Trees
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been replaced by a single Calculations dialog box.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. A new framework has
also been created for the score models used to calculate distances
between sequences. This framework allows import of substitution
matrices in NCBI and AAIndex format, and custom score models to be
created via a groovy script.
- 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 services have been updated, so
their options and parameters have changed.
- 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.
- Recent search histories for Find and the free
text search system (for querying Uniprot and the PDBe).
Experimental Features
This release of Jalview includes a new option in the Jalview Desktop
that allows you to try out features that are still in development.
To access the features described below, please first enable the Tools→Enable
Experimental Features option, and then restart 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.