jalview を Homebrew Cask でインストール

プロジェクトリンク

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• jalview

プロジェクトの歴史

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.

採用の歴史

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.

使われ方

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.

パッケージ好きにとっての重要性

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.

タイムライン

• 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

ソース

• https://www.jalview.org/about/archive/
• https://www.jalview.org/development/
• https://www.jalview.org/development/archive/
• https://www.jalview.org/help/html/
• https://www.jalview.org/tutorial/TheJalviewTutorial.pdf