Acacia

A web app for visualizing multiple sequence alignments (MSA) and phylogenetic trees. Built with React and TypeScript.

Features

• MSA viewer — renders large alignments efficiently using OffscreenCanvas in a Web Worker
• Phylogenetic tree viewer — interactive SVG tree with pan/zoom, reroot, and node collapse
• Neighbor-Joining — runs the NJ algorithm off the main thread via a dedicated worker (which in turn uses nj.rs)
• Combined view — side-by-side MSA and tree (Not implemented yet)
• Distances - All pairwise distances according to a selected substitution model.

Running locally

(Needs Node >= 20 and corresponding NPM)

git clone https://github.com/wur-bioinformatics/acacia
cd acacia
npm install
npm run dev

Stack

• React + TypeScript (Vite)
• Zustand for state management
• Tailwind + DaisyUI
• nj.rs (Rust/WASM) for Neighbor-Joining in the browser