Publications
Selected peer-reviewed papers and thesis, presented as on the Computational Phylogenomics Lab people page. DOIs are omitted here; use Google Scholar or ORCID for stable links.
Selected publications
01
2026
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
T.K.F. Wong, N. Ly-Trong, H. Ren, P. Demotte, H. Baños, A. Roger, E. Susko, C. Bielow, N. De Maio, N. Goldman, M.W. Hahn, M.d. Reis, L.S. Vinh, G. Huttley, R. Lanfear, B.Q. Minh
Molecular Biology and Evolution, 43:msag117 (2026)
02
2022
AliSim: A fast and versatile phylogenetic sequence simulator for the genomic era
N. Ly-Trong, S. Naser-Khdour, R. Lanfear, B.Q. Minh
Molecular Biology and Evolution, 39:msac092 (2022)
03
2024
Phylogenomics in the pandemic era
N. Ly-Trong
PhD Theses (2024)
04
2023
AliSim-HPC: Parallel sequence simulator for phylogenetics
N. Ly-Trong, G.M.J. Barca, B.Q. Minh
Bioinformatics, 39:btad540 (2023)
05
2024
CMAPLE: Efficient phylogenetic inference in the pandemic era
N. Ly-Trong, C. Bielow, N. De Maio, B.Q. Minh
Molecular Biology and Evolution, 41:msae134 (2024)
06
2025
Assessing phylogenetic confidence at pandemic scales
N. De Maio, N. Ly-Trong, S. Martin, B.Q. Minh, N. Goldman
Nature, 647:472–478 (2025)
07
2026
Rate variation and recurrent sequence errors in pandemic-scale phylogenetics
N. De Maio, M. Willemsen, S. Martin, Z. Guo, A. Saha, M. Hunt, N. Ly-Trong, B.Q. Minh, Z. Iqbal, N. Goldman
Nature Methods, 23:565–573 (2026)
08
2026
IQ-NET: Fast and Accurate Quartet Phylogenetic Inference Using Deep Learning Trained on Empirical DNA Alignments
C. Yang, Z. Zhuang, P. Demotte, C.C. Dang, L.S. Vinh, B.Q. Minh, N. Ly-Trong
Molecular Phylogenetics and Evolution (2026)
Preprints
The following items are preprints (not peer-reviewed journal articles). Listed as on the lab people page.
01
2024
TreeFormer: A transformer-based tree rearrangement operation for phylogenetic reconstruction
N. Ly-Trong, F. Albert Matsen IV, B.Q. Minh
bioRxiv (2024)
02
2025
IQ2MC: A New Framework to Infer Phylogenetic Time Trees Using IQ-TREE 3 and MCMCTree with Mixture Models
P. Demotte, M. Panchaksaram, H. Kumarasinghe, N. Ly-Trong, M.d. Reis, B.Q. Minh
EcoEvoRxiv (2025)
03
2026
Modeling Site-Specific Mutation Patterns in Pandemic-Scale Phylogenetics
S. Martin, N. Ly-Trong, B.Q. Minh, N. Goldman, N. De Maio
bioRxiv (2026)
04
2026
Tryptophan became part of the universal genetic code post-LUCA
S. Wehbi, N. Ly-Trong, A. Wheeler, B.Q. Minh, D. Lauretta, J. Masel
bioRxiv (2026)
05
2026
CMAPLE 2: Fast and Accurate Phylogenetic Inference for Millions of Pathogen Genomes
N. Ly-Trong, S. Martin, N. Goldman, N. De Maio, B.Q. Minh
bioRxiv (2026)
06
2026
GTRspmix: Capturing heterogeneity of exchangeabilities across sites to improve protein phylogenetics
R. Harada, E. Susko, T.K.F. Wong, H. Banos, N. Ly-Trong, R. Lanfear, D.L. Theobald, B.Q. Minh, A.J. Roger
bioRxiv (2026)
07
2026
ProtFinder: An efficient machine learning framework for protein model selection on real data
N.H. Tinh, Y. Dong, N. Ly-Trong, L.S. Vinh, B.Q. Minh
bioRxiv (2026)
See all publications on Google Scholar or ORCID. DOIs are not listed here pending verification — use those profiles for stable links. Google Scholar · ORCID · Lab profile