Publications

Preprints

  1. PartitionFinder-mAIC: Phylogenetic partitioning using marginal akaike information criterion
    H. Ren, T.K.F. Wong, C. Jiang, E. Susko, R. Lanfear, B.Q. Minh
    bioRxiv (2026)

  2. 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)

  3. 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)

  4. 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)

  5. 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)

  6. Modeling Site-Specific Mutation Patterns in Pandemic-Scale Phylogenetics
    S. Martin, N. Ly-Trong, B.Q. Minh, N. Goldman, N. De Maio
    bioRxiv (2026)

  7. A New Information Theoretic Approach Shows that Mixture Models Outperform Partitioned Models for Phylogenetic Analyses of Amino Acid Data
    H. Ren, C. Jiang, T.K.F. Wong, Y. Shao, E. Susko, B.Q. Minh, R. Lanfear
    bioRxiv (2026)

  8. 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)

  9. Robust Phylogenetics
    Q. Liu, B.Q. Minh, R. Lanfear, M.A. Charleston, S.A. Richards, B.R. Holland
    bioRxiv (2025)

  10. TreeFormer: A transformer-based tree rearrangement operation for phylogenetic reconstruction
    N. Ly-Trong, F. Albert Matsen IV, B.Q. Minh
    bioRxiv (2024)

Journal papers

    2026

  1. 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)

  2. IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models highly cited
    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)

  3. piqtree: A Python Package for Seamless Phylogenetic Inference with IQ-TREE
    R.N. McArthur, T.K.F. Wong, Y. Lang, R.A. Morris, K. Caley, V. Mallawaarachchi, B.Q. Minh, G.A. Huttley
    Molecular Biology and Evolution 43:msag061 (2026)

  4. 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)

  5. Phylogenetic Accuracy Under Non-Stationary and Non-Homogeneous Conditions: A Simulation Study
    S. Naser-Khdour, B.Q. Minh, R. Lanfear
    Systematic Biology syag010 (2026)

    6. 2025

  6. Assessing phylogenetic confidence at pandemic scales
    N. De Maio, N. Ly-Trong, S. Martin, B.Q. Minh, N. Goldman
    Nature 647:472–478 (2025)

  7. A robustly rooted tree of eukaryotes reveals their excavate ancestry highly cited
    K. Williamson, L. Eme, H. Baños, C. McCarthy, E. Susko, R. Kamikawa, R. Orr, S. Muñoz-Góme, B.Q. Minh, A. Simpson, A. Roger
    Nature 640:974–981 (2025)

  8. MixtureFinder: Estimating DNA mixture models for phylogenetic analyses
    H. Ren, T.K.F. Wong, B.Q. Minh, R. Lanfear
    Molecular Biology and Evolution 42:msae264 (2025)

    9. 2024

  9. Order of amino acid recruitment into the genetic code resolved by last universal common ancestor’s protein domains
    S. Wehbi, A. Wheeler, B. Morel, N. Manepalli, B.Q. Minh, D.S. Lauretta, J. Masel
    PNAS 121:e2410311121 (2024)

  10. GTRpmix: A linked general-time reversible model for profile mixture models
    H. Banos, T.K.F. Wong, J. Daneau, E. Susko, B.Q. Minh, R. Lanfear, M.W. Brown, L. Eme, A.J. Roger
    Molecular Biology and Evolution 92:msae134 (2024)

  11. 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)

  12. MAST: Phylogenetic Inference with Mixtures Across Sites and Trees
    T.K.F. Wong, C. Cherryh, A.G. Rodrigo, M.W. Hahn, B.Q. Minh, R. Lanfear
    Systematic Biology 73:375–391 (2024)

  13. Perianth evolution and implications for generic delimitation in the eucalypts (Myrtaceae), including the description of the new genus, *blakella*
    M.D. Crisp, B.Q. Minh, B. Choi, R.D. Edwards, J. Hereward, C. Kulheim, Y.P. Lin, K. Meusemann, A.H. Thornhill, A. Toon, L.G. Cook
    Journal of Systematics and Evolution 62:942-962 (2024)

  14. 2023 zuckerkandl prize
    C.M. Weisman, B.Q. Minh, D.A. Liberles
    Journal of Molecular Evolution 92:1-2 (2024)

    15. 2023

  15. AliSim-HPC: Parallel sequence simulator for phylogenetics
    N. Ly-Trong, G.M.J. Barca, B.Q. Minh
    Bioinformatics 39:btad540 (2023)

  16. DecentTree: Scalable Neighbour-Joining for the Genomic Era
    W. Wang, J. Barbetti, T.K.F. Wong, B. Thornlow, R. Corbett-Detig, Y. Turakhia, R. Lanfear, B.Q. Minh
    Bioinformatics 39:btad536 (2023)

  17. Maximum likelihood pandemic-scale phylogenetics
    N. De Maio, P. Kalaghatgi, Y. Turakhia, R. Corbett-Detig, B.Q. Minh, N. Goldman
    Nature Genetics 55:746–752 (2023)

  18. Updated site concordance factors minimize effects of homoplasy and taxon sampling highly cited
    Y.K. Mo, R. Lanfear, M.W. Hahn, B.Q. Minh
    Bioinformatics 39:btac741 (2023)

  19. 2022 Zuckerkandl Prize
    D.A. Liberles, D. Alvarez-Ponce, M.M. Meyer, B.Q. Minh, J.C. Silva
    Journal of Molecular Evolution 91:1-1 (2023)

    20. 2022

  20. AliSim: A fast and versatile phylogenetic sequence simulator for the genomic era highly cited
    N. Ly-Trong, S. Naser-Khdour, R. Lanfear, B.Q. Minh
    Molecular Biology and Evolution 39:msac092 (2022)

  21. nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models
    C.C. Dang, B.Q. Minh, H. McShea, J. Masel, J.E. James, L.S. Vinh, R. Lanfear
    Systematic Biology 71:1110-1123 (2022)

  22. Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals
    S. Naser-Khdour, B.Q. Minh, R. Lanfear
    Systematic Biology 71:959-972 (2022)

    23. 2021

  23. A comprehensive phylogenetic analysis of the serpin superfamily
    M.A. Spence, M.D. Mortimer, A.M. Buckle, B.Q. Minh, C.J. Jackson
    Molecular Biology and Evolution 38:2915–2929 (2021)

  24. Want to track pandemic variants faster? Fix the bioinformatics bottleneck highly cited
    E.B. Hodcroft, N. De Maio, R. Lanfear, D.R. MacCannell, B.Q. Minh, H.A. Schmidt, A. Stamatakis, N. Goldman, C. Dessimoz
    Nature 591:30-33 (2021)

  25. QMaker: Fast and accurate method to estimate empirical models of protein evolution highly cited
    B.Q. Minh, C. Cao Dang, L.S. Vinh, R. Lanfear
    Systematic Biology 70:1046–1060 (2021)

    26. 2020

  26. Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression highly cited
    D. Vanderpool, B.Q. Minh, R. Lanfear, D. Hughes, S. Murali, R.A. Harris, M. Raveendran, D.M. Muzny, M.S. Hibbins, R.J. Williamson, R.A. Gibbs, K.C. Worley, J. Rogers, M.W. Hahn
    PLOS Biology 18:e3000954 (2020)

  27. Newly Emerged Serotype 1c of Shigella flexneri: Multiple Origins and Changing Drug Resistance Landscape
    P. Parajuli, B.Q. Minh, N.K. Verma
    Genes 11:1042 (2020)

  28. Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution highly cited
    N. Dombrowski, T.A. Williams, J. Sun, B.J. Woodcroft, J. Lee, B.Q. Minh, C. Rinke, A. Spang
    Nature Communications 11:3939 (2020)

  29. New methods to calculate concordance factors for phylogenomic datasets highly cited
    B.Q. Minh, M.W. Hahn, R. Lanfear
    Molecular Biology and Evolution 37:2727-2733 (2020)

  30. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era highly cited
    B.Q. Minh, H.A. Schmidt, O. Chernomor, D. Schrempf, M.D. Woodhams, A. von Haeseler, R. Lanfear
    Molecular Biology and Evolution 37:1530-1534 (2020)

  31. GHOST: Recovering Historical Signal from Heterotachously Evolved Sequence Alignments highly cited
    S.M. Crotty, B.Q. Minh*, N.G. Bean, B.R. Holland, J. Tuke, L.S. Jermiin, A. von Haeseler (*co-first)
    Systematic Biology 69:249-264 (2020) Preprint

    32. 2019

  32. The Prevalence and Impact of Model Violations in Phylogenetic Analysis highly cited
    S. Naser-Khdour, B.Q. Minh, W. Zhang, E.A. Stone, R. Lanfear
    Genome Biology and Evolution 11:3341-3352 (2019)

  33. Polymorphism-Aware Species Trees with Advanced Mutation Models, Bootstrap, and Rate Heterogeneity
    D. Schrempf, B.Q. Minh, A. von Haeseler, C. Kosiol
    Molecular Biology and Evolution 36:1294-1301 (2019)

  34. Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase
    S. Schenk, S.C. Bannister, F.J. Sedlazeck, D. Anrather, B.Q. Minh, A. Bileck, M. Hartl, A. von Haeseler, C. Gerner, F. Raible, K. Tessmar-Raible
    eLife 8:e41556 (2019)

    35. 2018

  35. MPBoot: Fast phylogenetic maximum parsimony tree inference and bootstrap approximation highly cited
    D.T. Hoang, L.S. Vinh, T. Flouri, A. Stamatakis, A. von Haeseler, B.Q. Minh
    BMC Evolutionary Biology 18:11 (2018)

  36. Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes highly cited
    R.J.E. Alves, B.Q. Minh, T. Urich, A. von Haeseler, C. Schleper
    Nature Communications 9:1517 (2018)

  37. Complex Models of Sequence Evolution Require Accurate Estimators as Exemplified with the Invariable Site Plus Gamma Model
    L. Nguyen, A. von Haeseler, B.Q. Minh
    Systematic Biology 67:552-558 (2018)

  38. UFBoot2: Improving the Ultrafast Bootstrap Approximation highly cited
    D.T. Hoang, O. Chernomor, A. von Haeseler, B.Q. Minh⊛, L.S. Vinh (⊛co-last)
    Molecular Biology and Evolution 35:518-522 (2018)

  39. Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation highly cited
    H. Wang, B.Q. Minh*, E. Susko, A.J. Roger (*co-first)
    Systematic Biology 67:216-235 (2018)

    40. 2017

  40. HIV-1 Full-Genome Phylogenetics of Generalized Epidemics in Sub-Saharan Africa: Impact of Missing Nucleotide Characters in Next-Generation Sequences
    O. Ratmann, C. Wymant, C. Colijn, S. Danaviah, M. Essex, S. Frost, A. Gall, S. Gaseitsiwe, M.K. Grabowski, R. Gray, S. Guindon, A. von Haeseler, P. Kaleebu, M. Kendall, A. Kozlov, J. Manasa, B.Q. Minh, S. Moyo, V. Novitsky, R. Nsubuga, S. Pillay, T.C. Quinn, D. Serwadda, D. Ssemwanga, A. Stamatakis, J. Trifinopoulos, M. Wawer, A.L. Brown, T. de Oliveira, P. Kellam, D. Pillay, C. Fraser, on behalf of the PANGEA-HIV Consort
    AIDS Research and Human Retroviruses 33:1083-1098 (2017)

  41. ModelFinder: Fast model selection for accurate phylogenetic estimates highly cited
    S. Kalyaanamoorthy, B.Q. Minh*, T.K.F. Wong*, A. von Haeseler, L.S. Jermiin (*co-first)
    Nature Methods 14:587-589 (2017) Full text (PMC)

    42. 2016

  42. Reversible polymorphism-aware phylogenetic models and their application to tree inference
    D. Schrempf, B.Q. Minh, N. De Maio, A. von Haeseler, C. Kosiol
    Journal of Theoretical Biology 407:362-370 (2016)

  43. Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices highly cited
    O. Chernomor, A. von Haeseler, B.Q. Minh
    Systematic Biology 65:997-1008 (2016)

  44. W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis highly cited
    J. Trifinopoulos, L. Nguyen, A. von Haeseler, B.Q. Minh
    Nucleic Acids Research 44:W232-W235 (2016)

  45. Untangling the early diversification of eukaryotes: A phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista highly cited
    F. Burki, M. Kaplan, D.V. Tikhonenkov, V. Zlatogursky, B.Q. Minh, L.V. Radaykina, A. Smirnov, A.P. Mylnikov, P.J. Keeling
    Proceedings of the Royal Society B: Biological Sciences 283:20152802 (2016)

    46. 2015

  46. Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference
    O. Chernomor, B.Q. Minh, A. von Haeseler
    Journal of Computational Biology 22:1129-1142 (2015)

  47. Whole genome analysis of a Vietnamese trio
    D.T. Hai, N.D. Thanh, P.T.M. Trang, L.S. Quang, P.T.T. Hang, D.C. Cuong, H.K. Phuc, N.H. Duc, D.D. Dong, B.Q. Minh, P.B. Son, L.S. Vinh
    Journal of Biosciences 40:113-124 (2015)

  48. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies highly cited
    L. Nguyen, H.A. Schmidt, A. von Haeseler, B.Q. Minh
    Molecular Biology and Evolution 32:268-274 (2015)

  49. Split diversity in constrained conservation prioritization using integer linear programming
    O. Chernomor, B.Q. Minh⊛, F. Forest, S. Klaere, T. Ingram, M. Henzinger, A. von Haeseler (⊛co-last)
    Methods in Ecology and Evolution 6:83-91 (2015)

  50. The Phylogenetic Likelihood Library highly cited
    T. Flouri, F. Izquierdo-Carrasco, D. Darriba, A. Aberer, L. Nguyen, B.Q. Minh, A. von Haeseler, A. Stamatakis
    Systematic Biology 64:356-362 (2015)

    51. 2014

  51. A novel Fibroblast Growth Factor Receptor family member promotes neuronal outgrowth and synaptic plasticity in Aplysia
    D.D. Pollak, B.Q. Minh, A. Cicvaric, F.J. Monje
    Amino Acids 46:2477-2488 (2014)

  52. Discovery of the first light-dependent protochlorophyllide oxidoreductase in anoxygenic phototrophic bacteria: A genuine LPOR in anoxygenic phototrophic bacteria
    M. Kaschner, A. Loeschcke, J. Krause, B.Q. Minh, A. Heck, S. Endres, V. Svensson, A. Wirtz, A. von Haeseler, K. Jaeger, T. Drepper, U. Krauss
    Molecular Microbiology 93:1066-1078 (2014)

  53. Decisive Data Sets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects highly cited
    E. Dell’Ampio, K. Meusemann, N.U. Szucsich, R.S. Peters, B. Meyer, J. Borner, M. Petersen, A.J. Aberer, A. Stamatakis, M.G. Walzl, B.Q. Minh, A. von Haeseler, I. Ebersberger, G. Pass, B. Misof
    Molecular Biology and Evolution 31:239-249 (2014)

    54. 2013

  54. Ultrafast Approximation for Phylogenetic Bootstrap highly cited
    B.Q. Minh, M.A.T. Nguyen, A. von Haeseler
    Molecular Biology and Evolution 30:1188-1195 (2013)

    55. 2010

  55. Quantitative detection and typing of hepatitis D virus in human serum by real-time polymerase chain reaction and melting curve analysis
    J. Hofmann, K. Frenzel, B.Q. Minh, A. von Haeseler, A. Edelmann, S.R. Ross, T. Berg, D.H. Krüger, H. Meisel
    Diagnostic Microbiology and Infectious Disease 67:172-179 (2010)

    56. 2009

  56. Distribution and Phylogeny of Light-Oxygen-Voltage-Blue-Light-Signaling Proteins in the Three Kingdoms of Life highly cited
    U. Krauss, B.Q. Minh*, A. Losi, W. Gartner, T. Eggert, A. von Haeseler, K. Jaeger (*co-first)
    Journal of Bacteriology 191:7234-7242 (2009)

  57. Taxon Selection under Split Diversity
    B.Q. Minh, S. Klaere, A. von Haeseler
    Systematic Biology 58:586-594 (2009)

  58. Budgeted Phylogenetic Diversity on Circular Split Systems
    B.Q. Minh, F. Pardi, S. Klaere, A. von Haeseler
    IEEE/ACM Transactions on Computational Biology and Bioinformatics 6:22-29 (2009)

    59. 2006

  59. Phylogenetic Diversity within Seconds
    B.Q. Minh, S. Klaere, A. von Haeseler
    Systematic Biology 55:769-773 (2006)

    60. 2005

  60. pIQPNNI: Parallel reconstruction of large maximum likelihood phylogenies
    B.Q. Minh, L.S. Vinh, A. von Haeseler, H.A. Schmidt
    Bioinformatics 21:3794-3796 (2005)

Refereed conference papers

    2020

  1. pQMaker: Empirically estimating amino acid substitution models in a parallel environment
    N.D. Canh, C. Cao Dang, L.S. Vinh, B.Q. Minh, D.T. Hoang
    2020 12th International Conference on Knowledge and Systems Engineering (KSE) 324-329 (2020)

    2. 2016

  2. A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation
    D.T. Hoang, L.S. Vinh, T. Flouri, A. Stamatakis, A. von Haeseler, B.Q. Minh
    2016 Eighth International Conference on Knowledge and Systems Engineering (KSE) 1-6 (2016)

    3. 2015

  3. Building Population-Specific Reference Genomes: A Case Study of Vietnamese Reference Genome
    N.D. Thanh, P.T.M. Trang, D.T. Hai, N.H.A. Tuan, L.S. Quang, B.Q. Minh, D.Q. Minh, P.B. Son, L.S. Vinh
    2015 Seventh International Conference on Knowledge and Systems Engineering (KSE) 97-102 (2015)

    4. 2010

  4. SDA*: A Simple and Unifying Solution to Recent Bioinformatic Challenges for Conservation Genetics
    B.Q. Minh, S. Klaere, A. von Haeseler
    2010 Second International Conference on Knowledge and Systems Engineering 33-37 (2010)

Refereed book chapters

    2024

  1. Substitution and Partition Models in Phylogenetics
    D.A. Duchêne, B.Q. Minh
    Reference Module in Life Sciences, The Encyclopedia of Evolutionary Biology, 2nd Edition 1-11 (2024)

    2. 2016

  2. Split Diversity: Measuring and Optimizing Biodiversity Using Phylogenetic Split Networks
    O. Chernomor, S. Klaere, A. von Haeseler, B.Q. Minh
    Biodiversity Conservation and Phylogenetic Systematics 14:173-195 (2016)

    3. 2010

  3. ACOPHY: A Simple and General Ant Colony Optimization Approach for Phylogenetic Tree Reconstruction
    H.Q. Dinh, B.Q. Minh*, H.X. Huan, A. von Haeseler (*co-first)
    Swarm Intelligence 6234:360-367 (2010)

Theses

    2026

  1. SimTeller: Improving the Realism of Simulated DNA Alignments and Machine-Learning Detection for Simulated Alignments
    M. Zeng
    Master Theses (2026)

    2. 2024

  2. Phylogenomics in the pandemic era
    N. Ly-Trong
    PhD Theses (2024)

  3. Phylogenetic Model Selection via Machine Learning
    Y. Dong
    Master Theses (2024)

    4. 2023

  4. QuartetNet: Novel Phylogenetic Quartet Tree Reconstruction Using Neural Networks
    Z. Zhuang
    Honours Theses (2023)

    5. 2008

  5. Computational Methods in Biodiversity Conservation
    B.Q. Minh
    PhD Theses (2008)

Other reports

    2021

  1. A test statistic to quantify treelikeness in phylogenetics
    C. Cherryh, B.Q. Minh, R. Lanfear
    bioRxiv (2021)

    2. 2020

  2. Are fleas highly modified Mecoptera? Phylogenomic resolution of Antliophora (Insecta: Holometabola)
    K. Meusemann, M. Trautwein, F. Friedrich, R.G. Beutel, B.M. Wiegmann, A. Donath, L. Podsiadlowski, M. Petersen, O. Niehuis, C. Mayer, K.M. Bayless, S. Shin, S. Liu, O. Hlinka, B.Q. Minh, A. Kozlov, B. Morel, R.S. Peters, D. Bartel, S. Grove, X. Zhou, B. Misof, D.K. Yeates
    bioRxiv (2020)


© 2019-2027 Minh Bui Lab on Computational Phylogenomics @ School of Computing, Australian National University