Install mafft with Homebrew, apt, MacPorts, Nix

Project links

• Homepage
• Repository
• Upstream docs
• Package manager page

Commands and aliases

• einsi
• fftns
• fftnsi
• ginsi
• linsi
• mafft
• mafft-distance
• mafft-einsi
• mafft-fftns
• mafft-fftnsi
• mafft-ginsi
• mafft-homologs.rb
• mafft-linsi
• mafft-nwns
• mafft-nwnsi
• mafft-profile
• mafft-qinsi
• mafft-sparsecore.rb
• mafft-xinsi
• nwns
• nwnsi

Project history

MAFFT originated as a fast Fourier transform-based approach to multiple sequence alignment, described in the 2002 Nucleic Acids Research paper cited by the official site. Subsequent official references trace major method and usability improvements through version 5, version 6, version 7, PartTree for large alignments, RNA structural alignment, multithreading, adding unaligned sequences, over-alignment control, large-data workflows, MPI parallelization, and MAFFT-DASH.

The official manual documents MAFFT as a Unix-style command-line program with aliases such as `linsi`, `ginsi`, `einsi`, `fftnsi`, `fftns`, `nwns`, and `mafft-profile`, each exposing a different speed/accuracy tradeoff.

Adoption history

MAFFT became a standard bioinformatics command-line package because it covers both routine and high-accuracy multiple sequence alignment workflows. The official site links to web services at EBI, MPI Bioinformatics Toolkit, GenomeNet, SIB MyHits, T-REX, DDBJ WABI, and CIPRES, showing adoption beyond a single downloadable CLI.

Package managers matter for MAFFT because alignment tools are commonly installed into reproducible research environments, HPC systems, and workflow managers. The supplied package facts show distribution through Homebrew, Debian, MacPorts, Nix, and Ubuntu, while the official site maintains source, Linux, macOS, and Windows download paths.

How it is used

The basic invocation is `mafft input > output` with FASTA input. The official site recommends `mafft-linsi input > output` as an accurate option for up to roughly 200 sequences and `mafft input > output` as a fast option for larger alignments, with `mafft --auto input > output` for automatic strategy selection.

The manual organizes MAFFT around algorithm families: accuracy-oriented L-INS-i, G-INS-i, and E-INS-i; speed-oriented FFT-NS and NW-NS variants; PartTree for very large sequence counts; and profile alignment for group-to-group workflows.

Why package nerds care

MAFFT is one of those scientific CLI packages that anchors entire downstream workflows. It matters to package maintainers because it has many executable aliases, platform-specific source/binary packaging, a long citation trail, and users who care about exact version behavior for reproducibility.

Its history also illustrates a common bioinformatics packaging pattern: a command-line core, official web services, and many package-manager builds coexisting because researchers need both interactive alignment services and scriptable local installs.

Timeline

• 2002: Official references cite the original MAFFT fast Fourier transform alignment method in Nucleic Acids Research.
• 2005: Official references cite MAFFT version 5 accuracy improvements.
• 2007: Official manual updated on Jun 9, 2007.
• 2008: Official references cite recent developments outlining version 6.
• 2010: Official references cite multithreaded MAFFT.
• 2013: Official references cite MAFFT version 7 performance and usability improvements.
• 2018: Official references cite MPI parallelization for large-scale alignments.
• 2019: Official references cite MAFFT-DASH and the MAFFT online service.
• 2024: Official site lists MAFFT 7.526 as the latest version in Apr 2024.

Related projects

• MAFFT is related to ClustalW, T-Coffee, PRRN, GenomeNet alignment services, EBI and MPI MAFFT servers, Jalview, Pfam, BioRuby, Vienna RNA package extensions, MXSCARNA, and ProbConsRNA, many of which are linked or referenced from the official site.

Sources

• https://gitlab.com/sysimm/mafft
• https://mafft.cbrc.jp/alignment/software/
• https://mafft.cbrc.jp/alignment/software/manual/manual.html
• source_facts.package-manager