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Citing rust-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, the iterative-refinement strategies (L-INS-i / G-INS-i / E-INS-i), the scoring matrices, the PartTree heuristic for large datasets — all of it is theirs. This project is engineering on top of their science.

If you use rust-MAFFT in published work, you must cite the original MAFFT paper. The rust-MAFFT manuscript (in preparation for Bioinformatics) should be cited additionally once it is published — but the algorithmic foundation always remains the Katoh et al. work, and that citation never goes away.

Primary citation — MAFFT v7

Always required, regardless of which mode you use.

Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution, 30(4), 772–780. 10.1093/molbev/mst010

@article{Katoh2013,
  author  = {Katoh, Kazutaka and Standley, Daron M.},
  title   = {{MAFFT} Multiple Sequence Alignment Software Version 7:
             Improvements in Performance and Usability},
  journal = {Molecular Biology and Evolution},
  volume  = {30},
  number  = {4},
  pages   = {772--780},
  year    = {2013},
  doi     = {10.1093/molbev/mst010}
}

TY  - JOUR
AU  - Katoh, Kazutaka
AU  - Standley, Daron M.
PY  - 2013
TI  - MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
JO  - Molecular Biology and Evolution
VL  - 30
IS  - 4
SP  - 772
EP  - 780
DO  - 10.1093/molbev/mst010
ER  -

Foundational citation — original MAFFT (2002)

Cite this additionally if your work uses the FFT-NS-1 or FFT-NS-2 modes. These are the original FFT-based strategies that the 2002 paper introduced.

Katoh, K., Misawa, K., Kuma, K., & Miyata, T. (2002). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30(14), 3059–3066. 10.1093/nar/gkf436

@article{Katoh2002,
  author  = {Katoh, Kazutaka and Misawa, Kazuharu and
             Kuma, Kei-ichi and Miyata, Takashi},
  title   = {{MAFFT}: a novel method for rapid multiple sequence
             alignment based on fast {F}ourier transform},
  journal = {Nucleic Acids Research},
  volume  = {30},
  number  = {14},
  pages   = {3059--3066},
  year    = {2002},
  doi     = {10.1093/nar/gkf436}
}

Mode-specific citations

Cite these in addition to the primary citation when the corresponding mode is part of your analysis.

Iterative refinement (L-INS-i / G-INS-i / E-INS-i)

Introduced in MAFFT v5.

Katoh, K., Kuma, K., Toh, H., & Miyata, T. (2005). MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research, 33(2), 511–518. 10.1093/nar/gki198

@article{Katoh2005,
  author  = {Katoh, Kazutaka and Kuma, Kei-ichi and
             Toh, Hiroyuki and Miyata, Takashi},
  title   = {{MAFFT} version 5: improvement in accuracy of multiple
             sequence alignment},
  journal = {Nucleic Acids Research},
  volume  = {33},
  number  = {2},
  pages   = {511--518},
  year    = {2005},
  doi     = {10.1093/nar/gki198}
}

PartTree (--parttree / --dpparttree)

The fast guide-tree algorithm used for 10K+ sequence datasets.

Katoh, K., & Toh, H. (2007). PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. Bioinformatics, 23(3), 372–374. 10.1093/bioinformatics/btl592

@article{Katoh2007,
  author  = {Katoh, Kazutaka and Toh, Hiroyuki},
  title   = {{PartTree}: an algorithm to build an approximate tree
             from a large number of unaligned sequences},
  journal = {Bioinformatics},
  volume  = {23},
  number  = {3},
  pages   = {372--374},
  year    = {2007},
  doi     = {10.1093/bioinformatics/btl592}
}

CITATION.cff

For citation managers that support the Citation File Format, the canonical machine-readable record is at CITATION.cff in the repository root. GitHub also exposes a "Cite this repository" button on the project page that reads this file.

You can also generate plain-text or BibTeX from the CFF directly:

pip install cffconvert
cffconvert -f bibtex -i CITATION.cff
cffconvert -f apalike -i CITATION.cff

Citing the rust-MAFFT port

The rust-MAFFT manuscript is in preparation for Bioinformatics. Once published, the citation will appear here and CITATION.cff will be updated. Until then, please:

  1. Always cite Katoh & Standley 2013 — it is the algorithmic foundation.
  2. Optionally cite the rust-MAFFT GitHub release if you want to pin a reproducible version of the port (e.g. Goiriz, rust-MAFFT v0.2.0, https://github.com/luksgrin/rust-MAFFT, 2026). DOI-minting via Zenodo is on the roadmap.

Why both should be cited

A port that produces byte-identical output to its reference does not create new science — it engineers new accessibility, integrability, and language-ecosystem reach for existing science. The science belongs to the upstream authors; the engineering belongs to the port authors. Citing both reflects this division honestly and is the practice we ask everyone using rust-MAFFT to follow.