react-msaview (JBrowseMSA)

A multiple sequence alignment viewer, also known as JBrowseMSA.

Docs

See user guide

Demo

See ProteinBrowser for a full suite of protein analysis tools.

Packages

Package	Description
packages/lib	Main react-msaview React component
packages/app	Demo application (deployed at https://gmod.org/JBrowseMSA)
packages/cli	Command-line tools (InterProScan batch processing)
packages/msa-parsers	MSA file format parsers
packages/svgcanvas	SVG canvas rendering (ESM fork of svgcanvas)

Development

git clone https://github.com/GMOD/react-msaview
cd react-msaview
pnpm install

Run the demo app

pnpm dev

This starts the app with hot module reloading. Changes to packages/lib/src/ will automatically reload.

Build all packages

pnpm build

Run tests

pnpm test

Other commands

pnpm lint        # Run ESLint
pnpm format      # Format with Prettier
pnpm typecheck   # Typecheck all packages
pnpm clean       # Clean all dist folders

Programmatic usage, embedding, downloading from NPM

To install as a NPM package or CDN style bundle, see USAGE.md

Notes

This repo also supports https://github.com/GMOD/jbrowse-plugin-msaview which is a JBrowse 2 plugin for viewing MSAs.

This repo also builds on abrowse (https://github.com/ihh/abrowse) and phylo-react (https://www.npmjs.com/package/phylo-react).