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### MAFFT Alignment (`mafft-align`) Performs multiple sequence alignment over two or more input sequences using the bundled `mafft` command-line program. The selected algorithm variant is controlled by the `align_method` configuration field. The tool returns a typed `MSA` object containing the aligned sequences and their identifiers, with helpers for column statistics and serialisation to FASTA or A3M. #### API Reference

Source List of sequence strings (protein or nucleotide) to align. At least 2 sequences are required for alignment. Optional list of sequence identifiers. If not provided, sequences are assigned sequential IDs (seq\_0, seq\_1, ...).

Source `"auto"` (MAFFT picks by input size), `"localpair"` (L-INS-i), `"globalpair"` (G-INS-i), or `"genafpair"` (E-INS-i). Available options: `auto`, `localpair`, `globalpair`, `genafpair` Iterative-refinement cycles. `0` = no refinement; \~1000 enables the full \*-INS-i pipelines with `*pair` methods. Number of CPU threads for parallel processing. Verbatim `mafft` CLI tokens for niche flags (e.g. `["--retree", "3", "--reorder"]`). Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device to run the tool on. Maximum execution time in seconds. `None` waits indefinitely. Random seed. When set, tools run reproducibly up to small GPU float noise (see `BaseToolOutput.approx_equal`), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source The multiple sequence alignment result containing aligned sequences, sequence IDs, and original unaligned sequences. Aligned sequences with `-` characters indicating gaps. All sequences must have the same length. Identifiers for each sequence. Auto-generated as `seq_0`, `seq_1`, ... if not provided.

#### Applications This tool is appropriate for any analysis that benefits from a multiple sequence alignment of homologous protein or nucleotide sequences. Common downstream uses include phylogenetic-tree inference, conservation analysis over alignment columns to identify functionally important residues, homology modelling against a related reference, motif and domain discovery across a protein family, and variant-effect analysis in the context of the conserved structural and functional positions revealed by the alignment. #### Usage Tips * **`align_method="auto"` is the default and lets MAFFT select an algorithm based on input size.** Use `localpair` for sequences with a single conserved domain flanked by variable regions, `globalpair` for full-length homologs of similar length, and `genafpair` for multi-domain sequences separated by long unalignable regions. The `*pair` variants run in O(N^2) time and are appropriate for up to a few hundred sequences. * **`max_iterations=0` (the default) skips iterative refinement.** Raise it to enable the full `*-INS-i` refinement pipeline when paired with one of the `*pair` methods. A value around `1000` is appropriate for high-accuracy alignments of small to medium datasets. * **`threads=1` is the default; raise it on large alignments.** MAFFT parallelises both the all-against-all distance computation and the iterative refinement passes, so increasing the thread count yields substantial wall-time reductions on alignments of hundreds of sequences or longer. * **Inputs must contain at least two non-empty sequences.** The input validator hard-errors otherwise. Auto-generated identifiers default to `seq_0`, `seq_1`, and so on when `sequence_ids` is omitted. * **`extra_args` accepts verbatim `mafft` CLI tokens.** Pass any CLI flag not exposed as a typed field through this list (for example `["--retree", "3", "--reorder"]` to control the guide-tree rebuild schedule). Tokens are inserted before the input FASTA path and take precedence over MAFFT's own defaults.