macOS
Homebrew Caskverified · 100%
brew install --cask jalviewlocal Homebrew cask metadata
cask
Install jalview with Homebrew Cask
Multiple sequence alignment editor, visualiser, analysis and figure generator. Version 2.11.5.1 via Homebrew Cask; verified from local package data.
install
Additional install commands
overview
Package summary
Multiple sequence alignment editor, visualiser, analysis and figure generator
Project links
Commands and aliases
- jalview
history
Project history and usage
Jalview is an open-source bioinformatics workbench for editing, visualizing, analyzing, and publishing multiple sequence alignments and associated annotations or molecular structures.
Project history
Jalview was initially developed in 1996 by Michele Clamp, James Cuff, Steve Searle, and Geoff Barton at the University of Oxford and later the European Bioinformatics Institute.
BBSRC eScience funding in 2004 enabled Andrew Waterhouse and Jim Procter to re-engineer the application as Jalview 2 using contemporary Java and web technologies. Further BBSRC support continued from 2009, followed by a Wellcome Trust Biomedical Resource grant from 2014.
The project remains open source and primarily Java-based, with development conducted publicly through the official Jalview GitLab and associated issue tracker.
Adoption history
Jalview moved from its original late-1990s implementation to a substantially re-engineered Jalview 2 in 2005. Its combination of desktop editing, visualization, analysis services, and structure integration established it as a reusable workbench for sequence-alignment research and teaching.
Long-term institutional support, published scientific citations, training material, open development, and desktop installers across major operating systems have sustained its use in the bioinformatics community.
How it is used
Researchers use Jalview to inspect and edit multiple sequence alignments, apply color schemes, attach sequence features, invoke analysis services, view associated three-dimensional structures, and export publication figures.
Desktop preferences are normally stored in `.jalview_properties` in the user's home directory. Command-line users can select an alternative preferences file with `--props` for controlled or reproducible workflows.
Why package nerds care
Jalview is a durable example of scientific desktop software that bridges interactive visualization, web services, command-line automation, and reproducible research figures.
Its long release history, Java portability, open source, executable JARs, desktop installers, development channels, and JavaScript edition make its packaging evolution particularly interesting.
Timeline
- 1996: Initial Jalview development began at the University of Oxford.
- 2004: BBSRC eScience funding supported the re-engineering that became Jalview 2.
- 2005: Jalview 2 was released.
- 2009: The Jalview 2 workbench paper was published, and renewed BBSRC support began.
- 2010–2012: Google Summer of Code work expanded RNA alignment and secondary-structure capabilities.
- 2014: Development gained Wellcome Trust Biomedical Resource support.
Related projects
- JalviewJS
- Jmol
- JABAWS
- BioJava
Sources
security posture
No protected-tool coverage found yet
No matching local secret-handling manifest was found for jalview. Package metadata is still published here so future coverage has a stable package URL.
Install behavior
- No Homebrew post-install hook is recorded in formula metadata.
- No Homebrew bottle metadata was recorded.
Recommended review
Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.
local files
Configuration and credential file locations
These source-backed paths show where this package keeps local settings or durable credentials. Automic Vault can use them as review targets for secret scanning, migration, and command approval.
Configuration files
Config paths the tool may read or write during local use.
- Unix
~/.jalview_properties- Windows
%HOMEPATH%\.jalview_properties
executables
Installed executables
| Command | Kind | Exposure | Note |
|---|---|---|---|
jalview | binary | Homebrew cask binary | jalview |
freshness
Version and freshness
These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.
page generated2026-11-04
manager version2.11.5.1
manager updated
local dataok
upstreamnot checked
latest detectednot detected
- infoNo package-manager update timestamp was available.low confidence
- infoRelease/tag comparison is only available for GitHub repositories.https://www.jalview.org/none confidence
install metadata
Package metadata
| Package key | cask:jalview |
|---|---|
| Version | 2.11.5.1 |
| Package manager | Homebrew Cask |
| Package manager page | https://formulae.brew.sh/cask/jalview |
| Homepage | https://www.jalview.org/ |
| Upstream docs | https://www.jalview.org/ |
| Source archive | https://www.jalview.org/downloads/installers/release/Jalview-2_11_5_1-macos-aarch64-java_8.dmg |
| SHA-256 | 341a3b2e52cfc0512df6767892a9c1dc8a458dccab1256f3686b3ad9288a7f47 |
| Bottle | not recorded |
| Homebrew post-install | not defined |
| Service | none declared |
registry facts
Source database details
| Source Database | Homebrew cask API |
|---|---|
| Tap | homebrew/cask |
| Full Token | jalview |
| Names |
|
| Artifacts | |
| Deprecated | no |
| Disabled | no |
source trail
Generated from repository data
This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.
Combined YAML source
View the package source record on GitHub.
Used sources
- cross-ecosystem install command graph
- curated configuration and credential file locations
- curated package history
- package relationship graph
- package version freshness
- package-page enrichment