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Updated Oct 19, 2026

Utilities

Align nucleotide or protein sequences with MAFFT

mafft-align is an offline multiple-sequence alignment node using MAFFT.

Agent
Align nucleotide FASTAAlign protein FASTACompare supported alignment modes

overview

What mafft-align does

Supply unaligned nucleotide or protein FASTA and receive aligned FASTA plus the native MAFFT log.

auto is the default mode; fast and accurate (L-INS-i) are also exposed. The operation runs one thread, preserves input sequence order and makes no network calls.

Supply 2 to 200 unique sequence IDs with ungapped sequences, at most 200000 residues and 1 MiB. The native process has a 300-second limit. The output provides an alignment, without phylogenetic or clinical interpretation.

This packaged operation uses 7.526. Upstream license: BSD-3-Clause. The linked source identifies the actual program; this page documents the adapter's exposed contract.

source gitlab.com/sysimm/mafft/-/tree/ee9799916df6a5d5103d46d54933f8eb6d28e244

use cases

Where mafft-align fits

Align nucleotide FASTA

Align supplied nucleotide sequences while preserving their order.

Align protein FASTA

Select the protein alphabet for supplied protein FASTA.

Compare supported alignment modes

Choose auto, fast or accurate mode within the same bounded contract.

reference

mafft-align inputs and flags

3 inputs
NameTypeFlagDescription
sequencesFILE--sequencesUnaligned FASTA; 2-200 unique sequence IDs, at most 200000 total residues, 1 MiB.
modeSTRING--modeAlignment mode: auto (default), fast, or accurate (L-INS-i).
sequence-typeSTRING--sequence-typeSequence alphabet: nucleotide (default) or protein.

Showing key inputs. mafft-align exposes 3 inputs in total.

example

Run mafft-align

mafft-align · command
python3 /app/run.py --sequences ./input.txt --mode accurate --sequence-type nucleotide ./output

guidance

Choosing mafft-align

Use MAFFT to align supplied sequences. Mapping sequencing reads to a reference and estimating transcript abundance are separate operations.

faq

mafft-align questions

sequences: Unaligned FASTA; 2-200 unique sequence IDs, at most 200000 total residues, 1 MiB. mode: Alignment mode: auto (default), fast, or accurate (L-INS-i). sequence-type: Sequence alphabet: nucleotide (default) or protein.

Aligned FASTA and log. auto is the default mode; fast and accurate (L-INS-i) are also exposed. The operation runs one thread, preserves input sequence order and makes no network calls.

Supply 2 to 200 unique sequence IDs with ungapped sequences, at most 200000 residues and 1 MiB. The native process has a 300-second limit. The output provides an alignment, without phylogenetic or clinical interpretation.

Use MAFFT to align supplied sequences. Mapping sequencing reads to a reference and estimating transcript abundance are separate operations.

The public image repository includes download instructions for this version and a separate source/notices bundle. Its overview provides an immutable ORAS command, the expected bundle checksum and pinned upstream source directions. The bundle contains the original build recipe, runtime sources and retained component license notices. Image, source and license notice downloads.

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Run mafft-align yourself

The saved synthetic check verified three ordered sequences, unchanged ungapped residues and an alignment of 38 columns. The complete aligned FASTA is not retained as a page sample. The command shows the container entrypoint with example paths.

Open mafft-align in the libraryBuild a workflow with it

Facts on this page come from the live Trickest tool library.