Jalview - new installers, command line tool, and enhanced alphafold support

Dear Jalviewers!

We are delighted to announce that Jalview - the last major release in the 2.11 series - is now available. In addition to new features and (many) bug fixes, this release also includes updated installers for all major operating systems, native support for Apple Silicon, and an enhanced jalview command-line tool.

Major new capabilities include support for import, exploration and analysis computationally determined 3D structures and their predicted alignment error (PAE) matrices, and a brand new command line interface (CLI) allowing more efficient batch processing of alignments, annotation, 3D structure data, and new controls for generation of figures generated from multiple alignments and 3D structure views.

Job Alert !! We are currently looking for a part-time outreach & training officer to continue to develop Jalview and the Dundee Resource’s online and face-to-face training program, and a software engineer or Java enabled bioinformatician interested in helping develop Jalview. If you are interested in either position please get in contact with Geoff Barton or Jim Procter.

That’s all for now … please let us know of any issues you encounter with this new release, and of course any requests for improvement or new functionality !

Jim, Ben, Mateusz, and Geoff.

Dear Jalviewers - the first patch release of the 2.11.3 series is now available.

This patch addresses bugs in the uniprot sequence fetcher, double-click column-group selection for clustered predicted alignment error (PAE) matrices, autodiscovery of chimera and chimeraX and ensures the jalview command line tool provided by Jalview installations can be discovered on the path.