JBrowseMSA

An interactive multiple sequence alignment viewer with a phylogenetic tree, protein domains and many color schemes, scaling to alignments of tens of thousands of rows. Everything runs in the browser; nothing is uploaded.

Twelve NLRP1 orthologs, their InterPro domains overlaid, and the inferred tree beside them. The view opens on the NACHT domain, which every row carries. Drag the alignment to scroll, and the minimap along the top marks where the columns on screen sit in all 1,666.

• Standalone app — Open your own files: a FASTA, Stockholm, Clustal, A3M or EMF alignment, a Newick tree, and GFF3 or InterProScan JSON annotations, from your computer or a URL.
• Tutorials — Data preparation outside the viewer, from sequences to an alignment, a tree and annotations, each walkthrough ending on a link that opens the result. The index doubles as the gallery.
• User guide — Navigation, color schemes, tracks, exporting, and sharing a link to a view.
• CLI — react-msaview-cli builds domain and exon GFFs from InterPro, InterProScan or RefSeq, and exports an SVG with no browser.
• Embedding — The React component: props, the model API, and the UMD script tag.
• Examples — The embedding guide as running code: one page per usage pattern, each rendering the viewer beside the source that produced it.
• Layers — Highlights, data tracks and structure mappings you compute, carried in the snapshot for the viewer to draw.
• R package — The msaviewr htmlwidget, with ape, Biostrings, ggtree, treeio and Shiny interop.
• Python package — The msaview-widget anywidget for JupyterLab, Notebook, VS Code and Colab, with Biopython, numpy and pandas interop.