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  Menu entries for calculating PCA and different types of tree have been replaced by a single Calculations dialog box.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.

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.

• Annotation transfer between Chimera and Jalview
  Two new entries in the Chimera viewer's Chimera menu allow positional annotation to be exchanged 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.