Welcome to Jalview Version 2.11.4.2 (released 19 February 2025)!!
Jalview version 2.11.4.2 is the second patch release for the fourth in the minor-release trilogy planned for Jalview's 2.11 series.
The patch release addresses some critical compatibility issues when using Jalview on Windows machines, including window display and redraw issues on Windows 11, and internationalisation and path issues when launching jalview and saving/restoring Jmol structure views.
This minor release adds new capabilities for visualisation and clustering of protein secondary structure annotations, along with enhanced control of the display and analysis of secondary structure from different sources of 3D structure and prediction.
The Calculations dialog has also been revised to accommodate a new implementation of the spatial clustering method PASiMap (Su et al. 2022 Comp. Struc. Biotech.) which was added to Jalview by Thomas Morell and Jennifer Fleming.
Jalview 2.11.4 also has new installers and command line scripts that bring several minor improvements, and also makes it easier for IT admins to manage Jalview installations on computers used by many different people. New installations of Jalview will by default store updates in user's home directories, Automatic updates can also be disabled, and updates instead carried out using a new jalview_update command line tool.
Experimental features
This release includes experimental support (enabled in the Tools menu) for handling drag'n'drop of alignment, tree, annotations and feature file(s) onto the Jalview Desktop. They can also be dragged onto the Jalview icon.