Jalview 2.8.1

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WARNING! Downloading this JVL file might automatically switch your Jalview installation to version 2.8.1 (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 2.8.1?


New Features


  • Internationalisation of user interface (usually called i18n support) and translation for Spanish locale
  • Define/Undefine group on current selection with Ctrl-G/Shift Ctrl-G
  • Improved group creation/removal options in alignment/sequence Popup menu
  • Sensible precision for symbol distribution percentages shown in logo tooltip.
  • Annotation panel height set according to amount of annotation when alignment first opened


  • Interactive consensus RNA secondary structure prediction VIENNA RNAAliFold JABA 2.1 service
  • Select columns containing particular features from Feature Settings dialog
  • View all ‘representative’ PDB structures for selected sequences
  • Update Jalview project format:
    • New file extension for Jalview projects ‘.jvp’
    • Preserve sequence and annotation dataset (to store secondary structure annotation,etc)
    • Per group and alignment annotation and RNA helix colouring
  • New similarity measures for PCA and Tree calculation (PAM250)
  • Experimental support for retrieval and viewing of flanking regions for an alignment

Issues Resolved


  • logo keeps spinning and status remains at queued or running after job is cancelled
  • cannot export features from alignments imported from Jalview/VAMSAS projects
  • Buggy slider for web service parameters that take float values
  • Newly created RNA secondary structure line doesn’t have ‘display all symbols’ flag set
  • T-COFFEE alignment score shading scheme and other annotation shading not saved in Jalview project
  • Local file cannot be loaded in freshly downloaded Jalview
  • Jalview icon not shown on dock in Mountain Lion/Webstart
  • Load file from desktop file browser fails
  • Occasional NPE thrown when calculating large trees
  • Cannot reorder or slide sequences after dragging an alignment onto desktop
  • Colour by annotation dialog throws NPE after using ’extract scores’ function
  • Loading/cut’n’pasting an empty file leads to a grey alignment window
  • Disorder thresholds rendered incorrectly after performing IUPred disorder prediction
  • Multiple group annotated consensus rows shown when changing ’normalise logo’ display setting
  • Find shows blank dialog after ‘finished searching’ if nothing matches query
  • Null Pointer Exceptions raised when sorting by feature with lots of groups
  • Errors in Jmol console when structures in alignment don’t overlap
  • Not all working JABAWS services are shown in Jalview’s menu
  • JAVAWS version of Jalview fails to launch with ‘invalid literal/length code’
  • Annotation/RNA Helix colourschemes cannot be applied to alignment with groups (actually fixed in 2.8.0b1)
  • RNA Helices and T-Coffee Scores available as default colourscheme


  • Remove group option is shown even when selection is not a group
  • Apply to all groups ticked but colourscheme changes don’t affect groups
  • Documented RNA Helices and T-Coffee Scores as valid colourscheme name
  • Annotation labels drawn on sequence IDs when Annotation panel is not displayed
  • Increased font size for dropdown menus on OSX and embedded windows


  • Consensus sequence for alignments/groups with a single sequence were not calculated
  • annotation files that contain only groups imported as annotation and junk sequences
  • Fasta files with sequences containing ‘*’ incorrectly recognised as PFAM or BLC
  • conservation/PID slider apply all groups option doesn’t affect background (2.8.0b1)
  • redundancy highlighting is erratic at 0% and 100%
  • Remove gapped columns fails for sequences with ragged trailing gaps
  • AMSA annotation row with leading spaces is not registered correctly on import
  • Jalview crashes when selecting PCA analysis for certain alignments
  • Opening the colour by annotation dialog for an existing annotation based ‘use original colours’ colourscheme loses original colours setting