FAMSA2 enables accurate multiple sequence alignment at protein-universe scale

Gudys, A.; Zielezinski, A.; Notredame, C.; Deorowicz, S.

doi:10.1101/2025.07.15.664876

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bioRxiv · 10.1101/2025.07.15.664876

FAMSA2 enables accurate multiple sequence alignment at protein-universe scale

Gudys, A.·Zielezinski, A.·Notredame, C.·Deorowicz, S.

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Abstract

We introduce FAMSA2, an algorithm that produces high-accuracy multiple protein sequence alignments with unprecedented speed. Across structural, phylogenetic, and functional benchmarks, FAMSA2 matches or exceeds the accuracy of state-of-the-art tools while running up to 400 times faster and outperforming the fastest existing aligners. The ability of FAMSA2 to process 12 million sequences in 40 minutes on a 64 GB RAM workstation enables evolutionary and structural analyses at previously unattainable scales.

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Gudys, A., Zielezinski, A., Notredame, C., Deorowicz, S.. 2025-07-18. FAMSA2 enables accurate multiple sequence alignment at protein-universe scale. https://doi.org/10.1101/2025.07.15.664876

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