Jalview 2.5.1

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WARNING! Downloading this JVL file might automatically switch your Jalview installation to version 2.5.1 (without auto-updates).

To revert back to the Jalview RELEASE channel, please visit the Using the Jalview Launch file page.

Download the Jalview Launch file (.jvl) for version 2.5.1?


Issues Resolved

  • Alignment prettyprinter doesn’t cope with long sequence IDs
  • clustalx colourscheme colours Ds preferentially when both D+E are present in over 50% of the column
  • nucleic acid structures retrieved from PDB do not import correctly
  • More columns get selected than were clicked on when a number of columns are hidden
  • annotation label popup menu not providing correct add/hide/show options when rows are hidden or none are present
  • Stockholm format shown in list of readable formats, and parser copes better with alignments from RFAM.
  • CSV output of consensus only includes the percentage of all symbols if sequence logo display is enabled


  • annotation panel disappears when annotation is hidden/removed


  • Alignment view not redrawn properly when new alignment opened where annotation panel is visible but no annotations are present on alignment
  • pasted region containing hidden columns is incorrectly displayed in new alignment window
  • Jalview slow to complete operations when stdout is flooded (fix is to close the Jalview console)
  • typo in AlignmentFrame->View->Hide->all but selected Rregions menu item.
  • inconsistent group submenu and Format submenu entry ‘Un’ or ‘Non’conserved
  • Sequence feature settings are being shared by multiple distinct alignments
  • group annotation not recreated when tree partition is changed
  • double click on group annotation to select sequences does not propagate to associated trees
  • Mac OSX specific issues:
    • exception raised when mouse clicked on desktop window background
    • Desktop menu placed on menu bar and application name set correctly
    • sequence feature settings not wide enough for the save feature colourscheme button