Evidence map›Paper›PMID 41316476›Full record

ArticleGenome biology2025

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

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

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed.

  1. Article
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  3. Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Pinglu Zhang *Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China.
Tong Zhou *Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China.
Yanming WeiYangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, Zhejiang, 324000, China.
Qinzhong TianInstitute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China.
Yixiao ZhaiInstitute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China.
Yizheng WangInstitute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China.
Quan ZouInstitute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China.ORCID http://orcid.org/0000-0001-6406-1142
Furong Tang *Quzhou People's Hospital, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, Zhejiang, 324000, China. Furong.Tang@hotmail.com.
Ximei Luo *Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China. luoximei@uestc.edu.cn.ORCID http://orcid.org/0000-0003-2956-6799

Funding

Fellowship of China Postdoctoral Science Foundation 2023M731984Fellowship of China Postdoctoral Science Foundation 2024T170498Fellowship of China Postdoctoral Science Foundation GZB20230365Municipal Government of Quzhou 2024D001National Natural Science Foundation of China 62271353National Natural Science Foundation of China 62371347National Natural Science Foundation of China 62425107National Natural Science Foundation of China 62450002National Natural Science Foundation of China 62571375Zhejiang Provincial Natural Science Foundation of China LD24F020004Zhongguancun Academy project 20240101Zhongguancun Academy projects 20240310
6 · The paper itself

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.

Indexed as

GenomicsSARS-CoV-2Sequence AlignmentSoftwareAlgorithmsGenome, ViralHumansPhylogenyMultiple genome alignmentMultiple sequence alignmentPhylogeneticsStructural variants

Identifiers

PMID41316476
PMCPMC12664224

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.