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Jalview is the fourth patch release in the 2.11.2 series. It includes four new colourschemes for protein alignments (Kunzman et al. 2020 BMC Bioinformatics), a new client for the latest Uniprot Search API (released June 2022), updated build documentation and improved user experience when discovering models and experimental structures from 3D-Beacons.

New Features

  • New GECOS amino acid colourschemes flower, blossum, ocean and sunset
  • Migrated Uniprot Free Text Search to latest Uniprot search API
  • Improved Structure Chooser’s 3D-Beacons search button design and visual delay indicators
  • 3D beacons Fetch Uniprot References confirmation dialog is only shown when number of sequences exceeds a threshold
  • Warning when Jalview compiled for Java 1.8 is run in a Java 11+ JRE
  • Updated tldr; section of Jalview’s build documentation (doc/building.md)

Issues Resolved

  • buggy PCA plot axes rendering can make them appear to be non-orthogonal
  • Enable ‘All groups’ option when conservation slider is opened and ‘Colour All Groups’ is enabled in Colours menu