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rust-MAFFT

Pure-Rust port of MAFFT 7.526, byte-identical to the C reference.

Built on MAFFT

rust-MAFFT is a port — every algorithmic decision in this codebase traces back to work by Kazutaka Katoh and colleagues at CBRC. The FFT-anchored alignment algorithm, the iterative-refinement strategies, the scoring matrices, the PartTree heuristic — all of it is theirs. This project is engineering on top of their science. If you use it in published work, please cite the original MAFFT paper. See the Citation page for full details and BibTeX.

What it is

A complete rewrite of the MAFFT multiple sequence alignment toolchain in Rust — no unsafe, no C at runtime, no global state. Output matches C MAFFT 7.526 byte-for-byte across BAliBASE 3 (1930/1930 fixtures) for every supported mode: FFT-NS-2, FFT-NS-i, G-INS-i, L-INS-i, E-INS-i, PartTree, --add, --adjustdirection, and more.

Three ways to use it

  • As a Rust library

    cargo add mafft

    Programmatic access from any Rust project. See the Rust API on docs.rs.

  • As a Python package

    pip install pymafft

    Native bindings via PyO3. Drop-in Biopython interop. See the Python API.

  • As a CLI binary

    # via cargo
cargo install mafft-rs

# or via pip (also bundles the binary)
pip install pymafft

# or pre-built from GitHub releases

    See the CLI Reference.

Why byte-identity matters

MAFFT is the de facto MSA reference for bioinformatics workflows. A Rust port that drifts even one tie-break from the C output forces every downstream pipeline to choose: re-validate the rewrite, or maintain a parallel C dependency. Byte-identity removes that choice — the Rust binary is a drop-in replacement.

The Byte-identity page documents the design decisions, FFT tie-break ports, FP-order constraints, and cross-validation infrastructure (99 FFI test functions against the C implementation, compiled in-tree on the same platform).

Status

  • All standard modes: byte-identical across BAliBASE 3.
  • Stub-parity flags (--pdbidlist, --pdbfilelist): match C MAFFT's "temporarily unavailable, 2018/Dec." exit verbatim — these were disabled upstream.
  • DNA: byte-identical on nucleotide input too (pair-phase gap scale, dndpre offset, lowercase output, --nuc / --amino), including C's distinct --thread 1 refinement path.
  • In-memory API: mafft_rs::run_from_seqs / Mafft::run_seqs and pymafft.align(...) share the CLI's flag layer, so --auto, --adjustdirection, --nuc behave identically from Rust, Python and the shell.
  • Out of scope / residuals: see the architecture index.