Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2.
basic_science · Level V
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- Record sourced from PubMed, PMID 41981150.
- Also identified by DOI 10.1038/s41587-026-03095-3.
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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.