Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2
GudyĆ, Adam Zielezinski, Andrzej Notredame, Cedric Deorowicz, Sebastian
GudyĆ, Adam
Zielezinski, Andrzej
Notredame, Cedric
Deorowicz, Sebastian
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Computational Biology
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Journal article
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Abstract
We introduce FAMSA2, an algorithm that produces high-accuracy multiple-protein-sequence alignments at high speed. Across structural, phylogenetic and functional benchmarks, FAMSA2 matches or exceeds the accuracy of state-of-the-art tools while running 400 times faster on average than existing aligners. By combining progressive alignment with medoid clustering-based guide tree construction and a dissimilarity measure derived from the longest common subsequence, it enables scalable alignment of massive protein families.
Citation
A. GudyĆ, A. Zielezinski, C. Notredame, S. Deorowicz, "Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2," Nature Biotechnology, pp. 1-4, 2026, https://doi.org/10.1038/s41587-026-03095-3.
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Nature Biotechnology
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31 Biological Sciences, 3101 Biochemistry and Cell Biology, 3102 Bioinformatics and Computational Biology
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Springer Nature