MSEAVIEW is an interactive web application for uploading, visualizing, and exploring multiple sequence alignments (MSA), phylogenetic trees, and tabular or numeric datasets. It provides linked, customizable panels for in-depth sequence and evolutionary analysis—all in your browser.
Upload & visualize different data types
- MSA (.fasta/.fas): View alignments with colored residues and codon highlighting.
- Phylogenetic trees (.nwk/.nhx): Explore trees in Newick or NHX format.
- Tabular data (.csv/.tsv): Select numeric columns for histogram plotting.
- Numeric lists (.txt): Plot numeric data as histograms.
Flexible panel management
- Create, duplicate, remove, or rename panels dynamically.
- Arrange panels freely in a draggable, resizable grid layout.
- Save or load entire workspaces (panel data, layout, and links).
Link panels for synchronized exploration
- Link alignment, tree, or histogram panels.
- Hover over alignment columns, tree tips, or histogram bars to highlight corresponding elements in linked panels.
- Synchronized horizontal scrolling for linked alignments.
Rich visualization tools
- Alignment panels with codon view toggle, sequence label truncation, and residue coloring.
- Phylogenetic trees with NHX annotation support and tip highlighting.
- Histograms with interactive column selection for tabular data.
Export / import
- Save current workspace as a JSON file.
- Load previously saved workspaces for seamless continuation.
No installation required
- Available online at https://mseaview.com
Run the app locally:
npm install
npm run devVisit http://localhost:5173 and upload your files. Alternatively head directly to https://mseaview.com
├── index.html
├── package.json
├── postcss.config.js
├── public
│ ├── d3.min.js
│ └── index.html
├── src
│ ├── App.jsx
│ ├── components
│ │ ├── Histogram.jsx
│ │ └── PhyloTreeViewer.jsx
│ ├── index.css
│ ├── index.jsx
│ └── main.jsx
└── tailwind.config.js- Upload data: Use the top menu buttons to upload MSA, tree, or data files.
- Manage panels: Duplicate, remove, link, or rename panels from the panel headers.
- Customize layout: Drag and resize panels as needed.
- Save/load workspace: Save your session to a file or load a previous session.
- Link panels: Link two panels to synchronize highlights and scrolling.