Published November 15, 2023 | Version 2.11.3.0
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 2.11.3.0 (15 November 2023) was a significant release featuring a powerful next-generation command line interface with wild-card support for batch processing, interactive exploration of AlphaFold Predicted Alignment Error (PAE) matrices, and AlphaFold's standard confidence colourscheme. Key additions included native M1 macOS builds, a standard FlatLaf look-and-feel across platforms, ambiguous base colourscheme, and improved structure viewing capabilities. The release also enhanced 3D structure import, added PAE matrix clustering, and included extensive command-line improvements for image export and structure handling.

Files

Jalview_2.11.3.0.zip

Files (610.8 MB)

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md5:e3098d59c421e223b4649192faab89bd
48.2 MB Download
md5:ac72fc20b5aa1c6e8518a446557f26d4
53.9 MB Download
md5:6e82e8d9a04db25fc78438aadf2d1e18
236.0 MB Preview Download
md5:c015d4dbb3aa384818d3a571072df76a
227.4 MB Download
md5:c12816f53d97bc2b7fe2a87d898c7366
45.4 MB Download

Additional details

Related works

Is compiled by
Software: 10.5281/zenodo.15098346 (DOI)
Is part of
Software: 10.5281/zenodo.18652817 (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/G022682/1The 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