Published August 26, 2025 | Version 2.11.5.0
Software Open

Jalview

Authors/Creators

  • 1. Barton Group, Division of Computational Biology, School of Life Sciences, University of Dundee, Scotland, UK
  • 2. University of Konstance, Konstance, Germany
  • 3. University of Rennes, Rennes, France
  • 4. St. Olafs College, USA
  • 5. HAN University of Applied Sciences, Netherlands
  • 6. University of Vienna, Austria
  • 7. University of Santa Cruz, USA
  • 8. Universite Paris Saclay, France
  • 9. Barton Group, Division of Computational Biology, School of Life Sciences Research, College of Life Sciences, University of Dundee, Scotland, UK
  • 10. Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology
  • 11. Barton Group, School of Life Sciences Research, College of Life Sciences, University of Dundee, Scotland, UK
  • 12. School of Life Sciences Research, College of Life Sciences, University of Dundee, Scotland, UK
  • 13. Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
  • 14. Wellcome Trust Sanger Institute, Hinxton, Canbridge, UK
  • 15. School of Life Sciences, University of Dundee, Scotland, UK

Description

Jalview is a free cross-platform program for multiple sequence alignment editing, visualisation and analysis. Use it to align, view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.

Jalview 2.11.5.0 (26 August 2025) was the fifth and final minor release in the 2.11 series, introducing a new secondary structure explorer for comparing protein secondary structures from different 3D structure sources. Secondary structure consensus colouring was added for alignments and subgroups. The command line was enhanced to import, view, and superimpose multiple structures. The release included improved Windows 11 support, better handling of non-Latin characters in usernames and directories, and fixes for network drive path issues with Jmol. New sorting options by sequence description and improved Uniprot fetcher functionality were also added.

Files

Jalview_2.11.5.0.zip

Files (1.2 GB)

Name Size
md5:ed4093863e438ba73daa1232ead98990
592.4 MB Preview Download
md5:9e0ead922c4fe8399c5888e9ec104325
583.8 MB Download
md5:d9bb49d58e4afe08b622678f504a0a89
48.0 MB Download

Additional details

Related works

Is compiled by
Software: 10.5281/zenodo.15098346 (DOI)
Is part of
Software: 10.5281/zenodo.18652889 (DOI)
Is published in
Journal article: 10.1093/bioinformatics/btp033 (DOI)
References
Journal article: 10.1093/bioinformatics/btg430 (DOI)

Software

Repository URL
https://gitlab.jalview.org/jalview/jalview.git
Programming language
Java
Development Status
Active

References

  • https://www.jalview.org
  • 2020-2024 Wellcome Trust: 218259Z/19/Z The Jalview resource for biological sequence, structure and function analysis: 2019 and beyond.
  • Funding: 2014-2019 BBSRC: BB/L020742/1 The Jalview Resource for Sequence Analysis and Annotation.
  • Funding: 2013-2018 Wellcome Trust: 101651/Z/13/Z Extending The Jalview Resource for Biological Sequence Alignment and Analysis
  • Funding: 2009-2014 BBSRC: BB/G022682/1 The Jalview Resource for Sequence Analysis and Annotation - www.jalview.org.
  • Funding: 2004-2007 BBSRC: BBS/B/16542 Visualisation of Biological Sequences, Alignments and Structures - VAMSAS