mafft

MAFFT multiple sequence alignment — high-level Rust API.

This is the ergonomic entry point to the rust-MAFFT workspace. It re-exports the alignment engine, sequence types, and I/O helpers so most callers can use mafft::* and skip the sub-crate imports.

Acknowledgment. rust-MAFFT is a port of MAFFT by Kazutaka Katoh and colleagues (CBRC). The science is theirs. If you use this crate in published work, please cite Katoh & Standley 2013; full guidance at the project citation page.

Install

cargo add mafft

Usage

use mafft::{MafftEngine, AlignmentMode, read_fasta};

let input = read_fasta("input.fasta").unwrap();
let engine = MafftEngine::new(AlignmentMode::FftNs2);
let msa = engine.align(&input);

Available strategies

The command line's flag layer (cli feature)

--auto chooses the mode from the input; --adjustdirection flips strands before aligning; --nuc / --amino force the type and the case fold. To get exactly that behaviour in-process instead of re-deriving it, enable the cli feature and use mafft::cli, which re-exports the mafft-rs library:

mafft = { version = "0.1", features = ["cli"] }

use mafft::cli::{run_from_seqs, SilentProgress};
use mafft::{read_fasta};

let input = read_fasta("input.fasta").unwrap();
let msa = run_from_seqs(["mafft", "--auto", "--nuc"], &input, &SilentProgress).unwrap();

When to depend on a sub-crate instead

Use the underlying crates directly only when you need finer control:

• mafft-core — engine + modes (skip the I/O layer)
• mafft-align, mafft-tree, mafft-scoring, mafft-fft — internals

Related

• mafft-rs — standalone CLI: cargo install mafft-rs
• pymafft — Python bindings: pip install pymafft

License

MIT AND BSD-3-Clause (the upstream MAFFT C source is BSD-licensed).