Jalview

Jalview is a free, cross‑platform application for editing, visualising and analysing multiple sequence alignments. It supports DNA, RNA and protein sequences, offering linked views of aligned nucleic‑acid and protein products. Users can generate phylogenetic trees, perform principal component analysis, and explore molecular structures through integrated visualisation tools such as Jmol, VARNA, Chimera, ChimeraX and PyMOL. The program can automatically retrieve experimental or predicted 3D structures via the 3D‑Beacons network and fetch sequences and alignments from EMBL‑EBI databases.

The desktop version provides a graphical interface to the Jalview A Bioinformatics Analysis Web Services framework, enabling remote alignment and analysis services. A web‑based JalviewJS variant runs in browsers, compiled from the same Java codebase using Java2Script and SwingJS. The software is released under the GPL and is recognised by ELIXIR‑UK as a Tier 1 resource and a Recommended Interoperability Resource for protein structure and function.