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Install

rust-MAFFT ships through three independent channels. Pick whichever fits your workflow — they all produce byte-identical alignments.

Add the top-level mafft crate to your project:

cargo add mafft

mafft is a thin re-export of mafft-core, mafft-types, and mafft-io — most callers should depend on it and stay stable across workspace reorganisations. For finer control, depend on the sub-crates directly.

Verify:

use mafft::{MafftEngine, AlignmentMode, SequenceSet, Sequence};

let input = SequenceSet {
    sequences: vec![
        Sequence { name: "a".into(), data: b"ACDEFGHIK".to_vec() },
        Sequence { name: "b".into(), data: b"ACDEFHIK".to_vec() },
    ],
    seq_type: mafft::SeqType::Protein,
};
let msa = MafftEngine::new(AlignmentMode::FftNs2).align(&input);
assert_eq!(msa.sequences.len(), 2);

pip install pymafft

Wheels are published for Linux (x86_64, aarch64), macOS (Intel, Apple Silicon), and Windows (x86_64) across Python 3.9 – 3.13. The install also drops a mafft-rs console script on your $PATH — the same native binary, just reachable from any pip environment.

Verify:

import pymafft
result = pymafft.align(["ACDEFGHIK", "ACDEFHIK", "ACDHIK"])
print(result.to_fasta())

Three ways to get the standalone mafft-rs binary, in order of convenience:

# Option A: cargo (requires Rust toolchain)
cargo install mafft-rs

# Option B: pip (no Rust toolchain needed; also installs the
# Python bindings as a bonus)
pip install pymafft

# Option C: pre-built binary from the GitHub release page
# https://github.com/luksgrin/rust-MAFFT/releases

Verify:

mafft-rs --version
mafft-rs sample.fasta > aligned.fasta

Platform support

Channel Linux x86_64 Linux aarch64 macOS Intel macOS Apple Silicon Windows x86_64
Rust crate ✓ ✓ ✓ ✓ ✓
Python wheel ✓ ✓ ✓ ✓ ✓
Pre-built binary ✓ ✓ ✓ ✓ ✓

From source

git clone --recurse-submodules https://github.com/luksgrin/rust-MAFFT
cd rust-MAFFT
cargo build --release -p mafft-rs   # CLI
cargo test --workspace --exclude pymafft --release   # full test suite (537 tests + 7 ignored)

The mafft-upstream/ submodule pins the reference C MAFFT version that the FFI cross-validation harness builds against. It's only required for development — release builds compile zero C code.