JBrowseMSA
An interactive multiple sequence alignment viewer — phylogenetic tree, protein domains, and many color schemes, scaling to very large alignments. Everything runs in the browser; nothing is uploaded.
Documentation
User guide
Features, file formats, and a tour of the app.
Embedding
Add the viewer to your app: props, model API, UMD bundle.
JBrowse integration
Build a connected JBrowse session from any gene: collapsed-intron genome view, alignment, and AlphaFold structure.
Gallery
Alignments that tell a biological story, plus connected JBrowse sessions.
Examples
A live gallery of usage patterns with source.
Standalone app
Open your own alignment, tree, and domain annotations.
R package (msaviewr)
ape, Biostrings, ggtree, treeio, and Shiny interop.
CLI
Batch InterProScan → GFF domain annotations.