Clustal is a widely used, multiple sequence alignment program. This
is Clustal Omega, the latest addition to the Clustal family. It
offers a significant increase in scalability over previous versions,
allowing hundreds of thousands of sequences to be aligned in only a
few hours. In addition, the quality of alignments is superior to
previous versions, as measured by a range of popular benchmarks.

Clustal Omega is currently a command line-only tool, and is only
suitable for aligning protein sequences, not DNA or RNA.

If you like Clustal-Omega please cite:

Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R,
McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG.
Fast, scalable generation of high-quality protein multiple sequence
alignments using Clustal Omega. Mol Syst Biol. 2011 Oct 11;7:539. doi:
10.1038/msb.2011.75. PMID: 21988835.

This requires argtable.