CoChat
Sign Up
Cited by 12Genomics and Phylogenetic StudiesAlgorithms and Data CompressionFractal and DNA sequence analysis

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

Open access
Zhang, Pinglu, Zhou, Tong, Wei, Yanming, Tian, Qinzhong, Zhai, Yixiao, Wang, Yizheng, Zou, Quan, Tang, Furong +1 more·2025·Genome Biology
DOI 10.1186/s13059-025-03881-3PMC PMC12664224
Open this paper in CoChat — free accountOpen PDF

Abstract

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.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1186/s13059-025-03881-3

Cites

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • In evolutionary genomics, agentic pipelines can coordinate large-scale comparative analyses, automatically integrating genome alignments, phylogenetic inference, and functional annotation across thousands of species, while reflecting on inconsistencies between sequence-based and structure-based evolutionary signals.

    “In evolutionary genomics, agentic pipelines can coordinate large-scale comparative analyses, automatically integrating genome alignments, phylogenetic inference, and functional annotation across thousands of species, while reflecting on inconsistencies between sequence-based and structure-based evolutionary signals [4].”

    From The next paradigm in bioinformatics: a review of multi-agent systems and foundational models for end-to-end scientific discovery (2026) · cites this paper as [4]

    Split into 2 atoms — 0 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 1 unverifiable. Expand the claim to see per-atom verdicts.

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

The citation lists haven’t been fetched yet

References 55 · Cited by 12

Research works printed but not linked: 55

  1. [1]Members C-N, Partners. Database resources of the National Genomics Data Center, China National Center for Bioinformation in 2025. Nucleic Acids Res. 2024;53(D1):D30–44. PMC11701749 39530327 · DOI
  2. [2]Lewin HA, Robinson GE, Kress WJ, Baker WJ, Coddington J, Crandall KA, et al. Earth BioGenome Project: sequencing life for the future of life. Proc Natl Acad Sci U S A. 2018;115(17):4325–33. 29686065 PMC5924910 · DOI · Paper page
  3. [3]Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, et al. Ncbi taxonomy: a comprehensive update on curation, resources and tools. Database. 2020;2020:baaa062. 32761142 PMC7408187 · DOI · Paper page
  4. [4]Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021;592(7856):737–46. 33911273 PMC8081667 · DOI · Paper page
  5. [5]Armstrong J, Fiddes IT, Diekhans M, Paten B. Whole-genome alignment and comparative annotation. Annu Rev Anim Biosci. 2019;7(1):41–64. 30379572 PMC6450745 · DOI
  6. [6]Gibbs RA. The human genome project changed everything. Nat Rev Genet. 2020;21(10):575–6. 32770171 PMC7413016 · DOI
  7. [7]Logsdon GA, Vollger MR, Eichler EE. Long-read human genome sequencing and its applications. Nat Rev Genet. 2020;21(10):597–614. 32504078 PMC7877196 · DOI
  8. [8]Cui M, Liu Y, Yu X, Guo H, Jiang T, Wang Y, et al. MiniSNV: accurate and fast single nucleotide variant calling from nanopore sequencing data. Brief Bioinform. 2024;25(6):bbae473. 39331016 PMC11428505 · DOI
  9. [9]Zheng Z, Ren Y, Chen L, Wong AOK, Li S, Yu X, et al. Repun: an accurate small variant representation unification method for multiple sequencing platforms. Brief Bioinform. 2025;26(1):bbae613. PMC11586763 39584701 · DOI
  10. [10]Wang Y, Zhai Y, Ding Y, Zou Q. SBSM-Pro: support bio-sequence machine for proteins. Sci China Inf Sci. 2024;67(11):212106. · DOI
  11. [11]Tian Q, Zhang P, Zhai Y, Wang Y, Zou Q. Application and comparison of machine learning and database-Based methods in taxonomic classification of High-Throughput sequencing data. Genome Biol Evol. 2024;16(5):evae102. PMC11135637 38748485
  12. [12]Kille B, Balaji A, Sedlazeck FJ, Nute M, Treangen TJ. Multiple genome alignment in the telomere-to-telomere assembly era. Genome Biol. 2022;23(1):182. 36038949 PMC9421119 · DOI · Paper page
  13. [13]Zhang P, Liu H, Wei Y, Zhai Y, Tian Q, Zou Q. FMAlign2: a novel fast multiple nucleotide sequence alignment method for ultralong datasets. Bioinformatics. 2024;40(1):btae014. 38200554 PMC10809904 · DOI
  14. [14]Zhou T, Zhang P, Zou Q, Han W. HAlign 4: a new strategy for rapidly aligning millions of sequences. Bioinformatics. 2024;40(12). PMC11646084 39607773
  15. [16]Sahlin K, Baudeau T, Cazaux B, Marchet C. A survey of mapping algorithms in the long-reads era. Genome Biol. 2023;24(1):133. 37264447 PMC10236595 · DOI
  16. [17]Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10. 2231712 · DOI · Paper page
  17. [18]Smith TF, Waterman MS, Fitch WM. Comparative biosequence metrics. J Mol Evol. 1981;18:38–46. 7334527 · DOI
  18. [19]Kent WJ. BLAT–the BLAST-like alignment tool. Genome Res. 2002;12(4):656–64. 11932250 PMC187518
  19. [20]Kehr B, Weese D, Reinert K. STELLAR: fast and exact local alignments. BMC Bioinformatics. 2011;12(Suppl 9):S15. 22151882 PMC3283304 · DOI
  20. [21]Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, et al. Human-mouse alignments with BLASTZ. Genome Res. 2003;13(1):103–7. 12529312 PMC430961 · DOI
  21. [22]Kielbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011;21(3):487–93. 21209072 PMC3044862 · DOI
  22. [23]Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL. Alignment of whole genomes. Nucleic Acids Res. 1999;27(11):2369–76. 10325427 PMC148804 · DOI · Paper page
  23. [24]Brudno M, Chapman M, Gottgens B, Batzoglou S, Morgenstern B. Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics. 2003;4:66. 14693042 PMC521198 · DOI
  24. [25]Zhang P, Wei Y, Tian Q, Zou Q, Wang Y. Fast sequence alignment for centromere with RaMA. Genome Res. 2025;35(5):1209–18. PMC12047532 39939176
  25. [26]Bzikadze AV, Pevzner PA. UniAligner: a parameter-free framework for fast sequence alignment. Nat Methods. 2023;20(9):1346–54. 37580559 · DOI
  26. [27]Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution’s cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA. 2003;100(20):11484–9. 14500911 PMC208784 · DOI · Paper page
  27. [28]Treangen TJ, Messeguer X. M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. BMC Bioinformatics. 2006;7:433. 17022809 PMC1629028 · DOI
  28. [29]Darling AE, Mau B, Perna NT. ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE. 2010;5(6):e11147. 20593022 PMC2892488 · DOI · Paper page
  29. [30]Angiuoli SV, Salzberg SL. Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics. 2011;27(3):334–42. 21148543 PMC3031037 · DOI · Paper page
  30. [32]Naznooshsadat E, Elham P, Ali SZ. FAME: fast and memory efficient multiple sequences alignment tool through compatible chain of roots. Bioinformatics. 2020;36(12):3662–8. 32170927 · DOI
  31. [33]Treangen TJ, Ondov BD, Koren S, Phillippy AM. The harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol. 2014;15(11):524. 25410596 PMC4262987 · DOI
  32. [34]Bray N, Pachter L. MAVID: constrained ancestral alignment of multiple sequences. Genome Res. 2004;14(4):693–9. 15060012 PMC383315 · DOI
  33. [35]Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Program NCS, et al. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 2003;13(4):721–31. 12654723 PMC430158 · DOI · Paper page
  34. [36]Notredame C, Higgins DG, Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000;302(1):205–17. 10964570 · DOI
  35. [37]Paten B, Herrero J, Beal K, Fitzgerald S, Birney E. Enredo and pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res. 2008;18(11):1814–28. 18849524 PMC2577869 · DOI
  36. [38]Morgenstern B, Frech K, Dress A, Werner T. Dialign: finding local similarities by multiple sequence alignment. Bioinformatics. 1998;14(3):290–4. 9614273 · DOI
  37. [39]Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, et al. Fast statistical alignment. PLoS Comput Biol. 2009;5(5):e1000392. 19478997 PMC2684580 · DOI
  38. [40]Altschul SF. Gap costs for multiple sequence alignment. J Theor Biol. 1989;138(3):297–309. 2593679 · DOI
  39. [41]Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–7. 15034147 PMC390337 · DOI · Paper page
  40. [42]Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K, et al. Alignathon: a competitive assessment of whole-genome alignment methods. Genome Res. 2014;24(12):2077–89. 25273068 PMC4248324 · DOI · Paper page
  41. [43]Fletcher W, Yang Z. Indelible: a flexible simulator of biological sequence evolution. Mol Biol Evol. 2009;26(8):1879–88. 19423664 PMC2712615 · DOI
  42. [44]Tang F, Chao J, Wei Y, Yang F, Zhai Y, Xu L, et al. HAlign 3: fast multiple alignment of ultra-large numbers of similar DNA/RNA sequences. Mol Biol Evol. 2022;39(8):msac166. 35915051 PMC9372455 · DOI
  43. [45]Katoh K, Standley DM. Mafft multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80. 23329690 PMC3603318 · DOI · Paper page
  44. [46]Sievers F, Higgins DG. Clustal Omega, accurate alignment of very large numbers of sequences. Multiple Seq Alignment Methods. 2014;1079:105–16. 24170397
  45. [47]Kille B, Nute MG, Huang V, Kim E, Phillippy AM, Treangen TJ. Parsnp 2.0: scalable core-genome alignment for massive microbial datasets. Bioinformatics. 2024;40(5):btae311. 38724243 PMC11128092 · DOI
  46. [48]Lassmann T. Kalign 3: multiple sequence alignment of large datasets. Oxford University Press; 2020. PMC7703769 31665271
  47. [49]Ahrenfeldt J, Skaarup C, Hasman H, Pedersen AG, Aarestrup FM, Lund O. Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods. BMC Genomics. 2017;18(1):19. 28056767 PMC5217230 · DOI
  48. [50]Zhang C, Nielsen R, Mirarab S. ASTER: A package for Large-Scale phylogenomic reconstructions. Mol Biol Evol. 2025;42(8):msaf172. 40668947 PMC12343031 · DOI
  49. [51]Zhang C, Nielsen R, Mirarab S. CASTER: direct species tree inference from whole-genome alignments. Science. 2025;387(6737):eadk9688. 39847611 PMC12038793 · DOI
  50. [52]Kuderna LF, Gao H, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, et al. A global catalog of whole-genome diversity from 233 primate species. Science. 2023;380(6648):906–13. 37262161 PMC12120848 · DOI
  51. [53]Zhang C, Nielsen R. WASTER: Practical de novo phylogenomics from low-coverage short reads. bioRxiv [Preprint]. 2025:2025.01.20.633983. 10.1101/2025.01.20.633983. PMC13042278 41870206 · DOI
  52. [54]Wei Y, Zou Q, Tang F, Yu L. WMSA: a novel method for multiple sequence alignment of DNA sequences. Bioinformatics. 2022;38(22):5019–25. 36179076 · DOI
  53. [57]Bloom BH. Space/time trade-offs in hash coding with allowable errors. Commun ACM. 1970;13(7):422–6. · DOI
  54. [58]Zhang P, Zhou T, Zou Q, Luo X, HAlign-G. A rapid and low-memory multiple-genome aligner for large-scale closely related genomes. 2025. Github; https://github.com/malabz/HAlign-G. PMC12664224 41316476
  55. [59]Zhang P, Zhou T, Zou Q, Luo X. Dataset for HAlign-G: A rapid and low-memory multiple-genome aligner for large-scale closely related genomes. 2025. Zenodo; https://zenodo.org/records/17042774 PMC12664224 41316476

Authors
Zhang, P., Zhou, T., Wei, Y., Tian, Q., Zhai, Y., Wang, Y., Zou, Q., Tang, F., & Luo, X.
Affiliations
  • University of Electronic Science and Technology of China (CN)
  • Xidian University (CN)
  • Wenzhou Medical University (CN)
Corresponding author
  • Tang, Furong
  • Luo, Ximei
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2025-11-28
Volume
26
Issue
1
Pages
406-406
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/s13059-025-03881-3
PMC
PMC12664224
OpenAlex
W4416790249
Cited by
12
References
55
Citations by year
2026: 11 · 2025: 1
FWCI
3.61
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome biology (publishedVersion, cc-by-nc-nd)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • National Natural Science Foundation of China (62450002, 62425107, 62371347, 62271353, 62571375)
  • Zhejiang Provincial Natural Science Foundation of China (LD24F020004)
  • Municipal Government of Quzhou (2024D001)
  • Fellowship of China Postdoctoral Science Foundation (2023M731984, GZB20230365, 2024T170498)
  • Zhongguancun Academy projects (20240310)
  • Zhongguancun Academy project (20240101)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
Keywords
multiple genome alignment, STAR alignment, structural variant calling, SARS-CoV-2 genome, human chromosomes, phylogenetic tree construction, memory-efficient alignment
MeSH terms
SARS-CoV-2, Algorithms, Humans, Phylogeny, Software, Sequence Alignment, Genome, Viral, Genomics

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review