Jalview version 2.11.5.1 is a patch release for the fifth and (hopefully) final minor release in Jalview’s 2.11 series.

This patch addresses the following critical issues when running Jalview on Windows:

• Jalview’s getdown update system failed to work correctly for launching Jalview from a 2.11.4.0 installation
• Newly downloaded structures in Jmol were not correctly linked to the alignment.

Bug fixes and improvements also include use of the EBI-AlphaFold API for more robust retrieval of PAE matrices, incomplete export of alignments as SVG. Lastly, Jalview can now import ‘.a3m’ format alignments provided by EMBL-EBI’s AlphaFold Database, 3D structure modelling pipelines, and sequence search tools (e.g. mmseqs2).

Jalview 2.11.5

The main highlight for 2.11.5’s release is a new tree visualisation that allows deep exploration of the differences between protein secondary structures derived from distinct sources of 3D structure. This builds on earlier experimental work introduced in Jalview 2.11.4 developed by Renia Correya, the newest member of Jalview’s core developer team. Secondary structure consensus colouring is also possible for alignments and subgroups, allowing divergence to be more easily detected.

The Jalview 2.11.5 command line also has new options making it possible to import, view (and optionally superimpose) several structures associated with one or more sequences in the same structure view.

Several patches are also introduced with this release that address problems reported in 2.11.4.1. These include better support for Jalview running on Windows 11, bugs affecting installations where usernames or directories include characters outside the latin alphabet, and fixes for path issues when launching jalview and saving/restoring Jmol structure views on network drives.

Please note, some of these updates will not automatically apply to existing installations. You will need to update your Jalview installation by visiting https://www.jalview.org/download and downloading the Jalview 2.11.5.0 installer for your platform.

For the full list of new features and patches, please see the release notes

This will be the last minor release for the 2.11 series. Please let us know of problems that require urgent patches. All new developments and bug fixes will be targeted to our next major release, Jalview 2.12.