AlignmentForge — phylogenomic alignment & trimming studio

AlignmentForge is an interactive visual software tool for exploring, filtering, trimming, and curating multilocus phylogenomic alignments.

Interfaces

 

Left: The General Catalog interface displaying an overview of sequences and projects. Right: The detailed Sequence Alignment view showing the nucleotide matrix.

You can inspect sequences, filter them by quality, trim ends, and easily select the best data for your phylogenetic analysis directly in the browser or on your desktop.

▶ Try it in your browser — no installation, with example data.

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Running it

There are two ways to run AlignmentForge. They are the same application. Use the one you prefer.

	Use when
1. In a browser	Simplest. Nothing to install, works on any OS
2. As a desktop app	You want full local filesystem access, offline capability, and maximum performance

1. In a browser

Open https://phyloforge.github.io/AlignmentForge/. Click the folder icon to open a directory, then select a folder on your computer that contains alignment files.

AlignmentForge uploads nothing. The page reads the folder locally on your machine through the browser's file picker. Your data stays entirely on your device.

2. As a desktop app

Download the installer for your operating system (macOS, Windows, or Linux) from the latest release.

The desktop app gives you complete, unrestricted access to your local filesystem. It can seamlessly read massive folders and write your filtered output datasets back to disk without prompting you for browser permissions.

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Try it with the example datasets

You do not need your own alignments to see how AlignmentForge works. This repository ships with several real datasets so you can try out the software right away.

Exon-only alignments

public/example_data/exons/ — Ten exon-only PHYLIP alignment files for frog phylogenomics.

▶ Open it live

Get it	How
Browse it on GitHub	See the sample files
Download the whole repository	public/example_data/exons/ is inside it

UCE alignments

public/example_data/uces/ — Ten Ultraconserved Element (UCE) alignments for testing.

▶ Open it live

Get it	How
Browse it on GitHub	See the sample files
Download the whole repository	public/example_data/uces/ is inside it

All markers combined

public/example_data/all_markers/ — A mix of different marker types in a single folder.

▶ Open it live

Get it	How
Browse it on GitHub	See the sample files
Download the whole repository	public/example_data/all_markers/ is inside it

Loading an example on your machine

1. Download or clone this repository:

git clone https://github.com/PhyloForge/AlignmentForge.git

2. Open AlignmentForge (either the web or desktop version).
3. Click to open a folder.
4. Select AlignmentForge/public/example_data/exons or one of the other example folders.

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What to load into AlignmentForge

Select any directory on your computer that holds alignment files.

AlignmentForge reads these file types:

Format	Extensions
FASTA	.fa, .fasta, .fna, .ffn
PHYLIP	.phy, .phylip
NEXUS	.nex, .nexus
Detected from content	.aln, .txt

PHYLIP and NEXUS files can be sequential or interleaved. AlignmentForge searches the selected folder and up to three levels of subfolders. It skips hidden folders and files, and folders named node_modules, target, and __MACOSX.

Every sequence in an alignment must have the same length. AlignmentForge reports a file it cannot read and continues with the rest of the folder.

AlignmentForge reads nucleotide alignments only. It changes these symbols when it reads a file:

• . and * become - (gap).
• X becomes N (unknown base).

A NEXUS file can declare its own GAP, MISSING, and MATCHCHAR symbols. AlignmentForge reads those symbols first.

After you select a directory, the application scans it, calculates summary statistics, and shows a visual catalog of all your loci. You can then apply filters, trim alignments, inspect the alignment matrix view, and export your curated dataset.

Export needs the desktop app. The browser version keeps your data on your device and cannot write files to disk.

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Development

To build the software from source:

1. Install Node.js (v20+) and Rust.
2. Clone this repository.
3. Run npm install to install dependencies.
4. Run npm run dev to start the browser development server.
5. Run npm run tauri dev to start the desktop development application.

Checks

Command	What it does
npm run check	Runs every check below
npm run build	Typechecks and builds the web application
npm run lint	Runs ESLint over the frontend code
npm test	Runs the engine test suite
npm run check:display	Checks the viewer's codon helpers against the engine
npm run check:parity	Compares the browser engine with the desktop engine on the example data
npm run manifests:check	Verifies the example manifests are current
npm run icons	Rebuilds the desktop icons from public/logo.svg (macOS)

One engine, two builds

The trimming engine is written once, in Rust, under src-tauri/src. The desktop application links it directly. The browser runs the same code compiled to WebAssembly, spread across Web Workers so the loci are processed in parallel and the interface never blocks. The two builds therefore cannot disagree. npm run check:parity checks this. It runs both builds on the example data. It compares the summary and the viewer data of each locus. Run npm run build:wasm before it.

npm run build:wasm compiles the engine for the browser. npm run dev and npm run build do this for you, so you need the wasm32-unknown-unknown Rust target and wasm-pack:

rustup target add wasm32-unknown-unknown
cargo install wasm-pack

The browser once carried its own copy of the pipeline in TypeScript. That copy is gone. Only two small display helpers remain in TypeScript, because the viewer translates codons for every frame it draws; npm run check:display checks them against the engine's rules.