mafft-core

The MAFFT alignment engine, in pure Rust. Byte-identical to C MAFFT 7.526.

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 (including mode-specific references) at the project citation page.

MafftEngine, AlignmentMode, the progressive-alignment driver (merge_step_cached / Falign), iterative refinement (segmented NW/SW + oscillation detection), and the --add / --addfragments machinery for grafting new sequences into an existing MSA. Output matches the C reference byte-for-byte across BAliBASE 3 (1930/1930) for every supported mode.

Install

cargo add mafft-core

Most users want the top-level mafft crate, which re-exports the public surface here and is more stable across internal reorganisations. Depend on mafft-core directly when you want a smaller dependency footprint or you're embedding the engine without the I/O layer.

Example

use mafft_core::{MafftEngine, AlignmentMode};
use mafft_types::{Sequence, SequenceSet, SeqType};

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: SeqType::Protein,
};
let msa = MafftEngine::new(AlignmentMode::FftNs2).align(&input);
println!("aligned {} sequences to width {}", msa.sequences.len(), msa.width());

Documentation

API reference: docs.rs/mafft-core

Project documentation: luksgrin.github.io/rust-MAFFT · Byte-identity design notes

License

MIT for the Rust port; the alignment algorithms are derived from upstream MAFFT under BSD-3-Clause. See LICENSE-MIT and LICENSE-BSD in the workspace root.