A Python wrapper for MAFFT

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MAFFTpy

Multiple sequence alignment. This is a Python wrapper for MAFFT.

The GUI is no longer distributed with this package. For the legacy executables, see below.

Installation

MAFFTpy is available on PyPI. You can install it through pip:

pip install itaxotools-mafftpy

Executables

Download and run the legacy executables without installing Python from the MAFFTpy release page.

No executables are currently provided for the command-line tool, which is only available after installation.

Usage

The package comes with a command-line tool:

mafftpy examples/brygoo.fas aligned.fas
mafftpy-fftns1 --adjustdirectionaccurately examples/brygoo.fas

The following limited features from MAFFT are available:

two strategies: FFT-NS-1 and G-INS-i
two options: --adjustdirection and --adjustdirectionaccurately

To use the Python API, import itaxotools.mafftpy.MultipleSequenceAlignment and use the start() method.

Dependencies

Building from source requires a C++ compiler (GCC, msvc)

In addition, pthread-win32 is required for Windows and is included as a git submodule.

Citation

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.

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0.3.0

Aug 23, 2025

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