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<p>HAlign-G is a fast and memory-efficient tool for large-scale multiple genome alignment. Using BWT-FM-LIS with an optimized K-band algorithm and star alignment strategy, it supports intra-species (HAlign-G1) and cross-species (HAlign-G2) alignment. Benchmarks show superior accuracy, efficiency, and memory use compared with existing methods. HAlign-G1 excels in speed and quality for intra-species data for multiple sequence alignment, while HAlign-G2 offers higher accuracy and structural variant detection for multiple genome alignment. Both versions handle millions of SARS-CoV-2 genomes and thousands of human chromosomes, enabling reliable evolutionary studies and supporting the construction of more stable phylogenetic trees, while enhancing Progressive Cactus performance.</p>

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HAlign-G: rapid and low-memory multiple-genome aligner for large-scale closely related genomes

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年11月28日

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  • Pinglu Zhang,
  • Tong Zhou,
  • Yanming Wei,
  • Qinzhong Tian,
  • Yixiao Zhai,
  • Yizheng Wang,
  • Quan Zou,
  • Furong Tang,
  • Ximei Luo

摘要

HAlign-G is a fast and memory-efficient tool for large-scale multiple genome alignment. Using BWT-FM-LIS with an optimized K-band algorithm and star alignment strategy, it supports intra-species (HAlign-G1) and cross-species (HAlign-G2) alignment. Benchmarks show superior accuracy, efficiency, and memory use compared with existing methods. HAlign-G1 excels in speed and quality for intra-species data for multiple sequence alignment, while HAlign-G2 offers higher accuracy and structural variant detection for multiple genome alignment. Both versions handle millions of SARS-CoV-2 genomes and thousands of human chromosomes, enabling reliable evolutionary studies and supporting the construction of more stable phylogenetic trees, while enhancing Progressive Cactus performance.