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<p>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.</p>

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Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2

  • 期刊论文

  • 发表日期：

    2026年4月14日

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  • Adam Gudyś,
  • Andrzej Zielezinski,
  • Cedric Notredame,
  • Sebastian Deorowicz

摘要

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.