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Author

Nhan Ly-Trong

Observed names: Ly, Trong Nhan, Ly-Trong, Nhan, Nhan LY-TRONG, Nhan Ly Trong
ORCID: 0000-0001-5668-5027
Observed ORCID: 0000-0001-5668-5027
OpenAlex ID: A5072480273
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
2025 · Wong. Thomas K.F., Ly-Trong, Nhan, et al. · EcoEvoRxiv · 862
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IQ-TREE 3: phylogenomic inference software using complex evolutionary models
2026 · Thomas K F Wong, Nhan Ly-Trong, et al. · Molecular Biology and Evolution · 530
AliSim: A Fast and Versatile Phylogenetic Sequence Simulator for the Genomic Era
2022 · Nhan Ly-Trong, Suha Naser-Khdour, et al. · Molecular Biology and Evolution · 119
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AliSim-HPC: parallel sequence simulator for phylogenetics
2023 · Nhan Ly-Trong, Giuseppe M J Barca, et al. · Bioinformatics · 21
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Towards a large-scale IoT Emulation Testbed based on Container Technology
2018 · Nhan LY-TRONG, Chuong DANG-LE-BAO, et al. · International Conference on Communications and Electronics (ICCE) · 15
CMAPLE: Efficient Phylogenetic Inference in the Pandemic Era
2024 · Nhan Ly-Trong, Chris Bielow, et al. · Molecular Biology and Evolution · 13
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Assessing phylogenetic confidence at pandemic scales
2025 · Nicola De Maio, Nhan Ly-Trong, et al. · Nature · 12
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Rate variation and recurrent sequence errors in pandemic-scale phylogenetics
2026 · Nicola De Maio, Myrthe Willemsen, et al. · Nature Methods · 10
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UiTiOt v3: A Hybrid Testbed for Evaluation of Large-Scale IoT Networks
2018 · Nhan Ly-Trong, Chuong Dang-Le-Bao, et al. · International Symposium on Information and Communication Technology · 7
IQ2MC: A New Framework to Infer Phylogenetic Time Trees Using IQ-TREE 3 and MCMCTree with Mixture Models
2025 · Piyumal Demotte, Muthukumaran Panchaksaram, et al. · 6
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UiTiOt: A Container-Based Network Emulation Testbed
2017 · Chuong Dang Le Bao, Nhan Ly Trong, et al. · International Conference on Machine Learning and Soft Computing (ICMLSC) · 5
TreeFormer: A transformer-based tree rearrangement operation for phylogenetic reconstruction
2024 · Nhan Ly-Trong, Frederick A. Matsen, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 3
GTRspmix: Capturing Heterogeneity of Exchangeabilities Across Sites to Improve Protein Phylogenetics
2026 · Ryo Harada, Edward Susko, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 2
Evaluation on UiTiOt Container-Based Emulation Testbed
2018 · Chuong Dang-Le-Bao, Nhan Ly-Trong, et al. · Lecture notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering · 2
IQ-NET: fast and accurate quartet phylogenetic inference using deep learning trained on empirical DNA alignments
2026 · Chen Yang, Zixin Zhuang, et al. · Molecular Phylogenetics and Evolution · 1
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CMAPLE 2: Fast and Accurate Phylogenetic Inference for Millions of Pathogen Genomes
2026 · Nhan Ly-Trong, Samuel Martin, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 1
Tryptophan became part of the universal genetic code post-LUCA
2026 · Sawsan Wehbi, Nhan Ly-Trong, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 1
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Modeling Site-Specific Mutation Patterns in Pandemic-Scale Phylogenetics
2026 · Samuel Martin, Nhan Ly-Trong, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 1
Fast and Accurate Quartet Phylogenetic Inference Using Deep Learning Trained on Empirical DNA Alignments
2026 · Chen Yang, Zixin Zhuang, et al. · Figshare
ProtFinder: An efficient machine learning framework for protein model selection on real data
2026 · Nguyen Huy Tinh, Yanghe Dong, et al. · bioRxiv (Cold Spring Harbor Laboratory)
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Phylogeny-aided detection of contamination in nearly 5 million SARS-CoV-2 genomes
2026 · Olivier Anoufa, Nhan Ly-Trong, et al. · bioRxiv (Cold Spring Harbor Laboratory)
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CMAPLE 2 Data
2026 · Ly-Trong, Nhan, Martin, Samuel, et al. · Zenodo (CERN European Organization for Nuclear Research)
Phylogeny-aided detection of contamination in nearly 5 million SARS-CoV-2 genomes
2026 · Anoufa, Olivier, Ly-Trong, Nhan, et al. · Zenodo (CERN European Organization for Nuclear Research)
IQ-NET: Fast and Accurate Quartet Phylogenetic Inference Using Deep Learning Trained on Empirical DNA Alignments
2026 · Yang, Chen, Zhuang, Zixin, et al. · Zenodo (CERN European Organization for Nuclear Research)
SliferSkyd/iqtree2: hPartition release
2026 · Bui Quang Minh, Lam-Tung Nguyen, et al. · Zenodo (CERN European Organization for Nuclear Research)
Works count: 30
Citation count: 1,612
H-index: 8
I10-index: 8
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