{"id":"W4409216400","doi":"10.1093/molbev/msag117","title":"IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models","year":2025,"lang":"en","type":"preprint","venue":"Molecular Biology and Evolution","topic":"Evolution and Genetic Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":331,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University","funders":"Centre for Innovation in Biomedical Imaging Technology, Australian Research Council; National Cancer Institute; Biotechnology and Biological Sciences Research Council; Natural Sciences and Engineering Research Council of Canada; Medical Research Council; Chan Zuckerberg Initiative; National Institute for Health and Care Research; Centre of Excellence for Quantum Computation and Communication Technology, Australian Research Council; National Computational Infrastructure; EMBL Australia; National Foundation for Science and Technology Development; European Molecular Biology Laboratory; Australian Government; Gordon and Betty Moore Foundation; National Science Foundation","keywords":"Inference; Computer science; Tree (set theory); Software evolution; Phylogenomics; Software; Machine learning; Artificial intelligence; Phylogenetics; Biology; Programming language; Software development; Mathematics; Clade; Genetics","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002979745,0.002393098,0.002448463,0.003079498,0.001326432,0.003644356,0.004984585,0.002058649,0.06951226],"category_scores_gemma":[0.01205138,0.002377591,0.00303613,0.003392916,0.0007883395,0.004221356,0.003718012,0.004898683,0.03822242],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008949272,"about_ca_system_score_gemma":0.002460196,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00446153,"about_ca_topic_score_gemma":0.00518784,"domain_scores_codex":[0.9990546,0.0002136597,0.00009454691,0.0002791417,0.0002548082,0.0001031472],"domain_scores_gemma":[0.9976058,0.001419131,0.0001894886,0.0003747958,0.000288653,0.0001222105],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0007533298,0.0002098707,0.008227365,0.004106428,0.001282801,0.0007977035,0.001622008,0.04350604,0.01282893,0.05425302,0.7154126,0.1569999],"study_design_scores_gemma":[0.0007282835,0.0001035062,0.005247789,0.0006246982,0.0004393968,0.001193485,0.000327511,0.3452926,0.01127974,0.1523325,0.4820592,0.0003713991],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.006092501,0.0007104094,0.5488923,0.0004452462,0.0003476574,0.0002046879,0.0731058,0.3636335,0.006567845],"genre_scores_gemma":[0.04647694,0.0009459524,0.5934104,0.000708981,0.000188289,0.001138435,0.1571494,0.1939746,0.006007087],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.06951226,"threshold_uncertainty_score":0.2325416,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0224946551662297,"score_gpt":0.3060605985958865,"score_spread":0.2835659434296569,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}