pymafft 0.1.0

Python bindings for MAFFT-rs multiple sequence alignment

pymafft

Python bindings for MAFFT-rs, a Rust reimplementation of the MAFFT multiple sequence alignment tool.

Installation

pip install pymafft

Quick start

import pymafft

# Align protein sequences
result = pymafft.align([
    "ACDEFGHIKLMNPQRSTVWY",
    "ACDEFHIKLMNPQRSTVWY",
    "ACDEHIKLMNPQRSTVWY",
])

for seq in result:
    print(f"{seq.name}: {seq.sequence}")

print(f"Alignment width: {result.width}")

Usage

Align from a list of sequences

# Auto-named (seq_1, seq_2, ...)
result = pymafft.align(["ACDEFGHIK", "ACDEFHIK", "ACDHIK"])

# Named sequences
result = pymafft.align([
    ("human", "ACDEFGHIKLMNP"),
    ("mouse", "ACDEFHIKLMNP"),
    ("fish",  "ACDEHIKLMNP"),
])

Align from a FASTA file

result = pymafft.align_file("sequences.fasta")

Align from a FASTA string

fasta = ">s1\nACDEFGHIK\n>s2\nACDEFHIK\n"
result = pymafft.align_fasta_string(fasta)

Choose an alignment strategy

# FFT-NS-2: fast default
result = pymafft.align(seqs, strategy="fftns2")

# G-INS-i: global iterative (accurate, for globally alignable sequences)
result = pymafft.align(seqs, strategy="ginsi")

# L-INS-i: local iterative (most accurate for <200 sequences)
result = pymafft.align(seqs, strategy="linsi")

# E-INS-i: generalized affine (for sequences with large internal gaps)
result = pymafft.align(seqs, strategy="einsi")

# FFT-NS-i: progressive + iterative refinement
result = pymafft.align(seqs, strategy="fftnsi", maxiterate=100)

Work with results

result = pymafft.align(["ACDEFGHIK", "ACDEFHIK"])

# Access sequences
result.nseq              # number of sequences
result.width             # alignment width (columns)
result[0].name           # sequence name
result[0].sequence       # aligned sequence (with gaps)
result[0].ungapped()     # sequence without gaps

# Export
result.to_fasta()        # FASTA-formatted string
result.to_tuples()       # list of (name, sequence) tuples

# Iterate
for seq in result:
    print(seq.name, len(seq))

Supported strategies

Strategy	Flag	Description
fftns2	default	Fast progressive alignment
fftnsi	--maxiterate N	Progressive + iterative refinement
ginsi	--globalpair	Global iterative (accurate)
linsi	--localpair	Local iterative (most accurate for <200 seqs)
einsi	--genafpair	Generalized affine (large internal gaps)

License

• Rust code: MIT
• Original MAFFT algorithm: BSD-3-Clause

Based on MAFFT by Kazutaka Katoh.