{"id":"W2106947130","doi":"10.1093/sysbio/syp054","title":"Species Trees from Highly Incongruent Gene Trees in Rice","year":2009,"lang":"en","type":"article","venue":"Systematic Biology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":122,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ontario Institute for Cancer Research","funders":"","keywords":"Biology; Phylogenetic tree; Evolutionary biology; Inference; Tree (set theory); Bayesian probability; Phylogenetics; Gene; Computational biology; Pipeline (software); Supermatrix; Genetics; Artificial intelligence; Computer science; Mathematics","routes":{"ca_aff":true,"ca_fund":false,"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":[0.006027754,0.0004282846,0.0006997302,0.004310315,0.001464562,0.001821992,0.0009718923,0.0005903193,0.0007434258],"category_scores_gemma":[0.02592377,0.0006937575,0.0008413021,0.003048232,0.001209769,0.001691471,0.001630118,0.001122549,0.0002181622],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008701714,"about_ca_system_score_gemma":0.000858388,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002136279,"about_ca_topic_score_gemma":0.00417527,"domain_scores_codex":[0.9979421,0.001022812,0.0001504227,0.0003559903,0.000430328,0.0000983615],"domain_scores_gemma":[0.9873276,0.008700936,0.001850609,0.0008926376,0.0007964681,0.000431772],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.002221948,0.00036651,0.3456452,0.001663578,0.001643115,0.001613422,0.01071663,0.2271726,0.1154753,0.04386217,0.002603601,0.247016],"study_design_scores_gemma":[0.0001206396,0.0001633988,0.2154996,0.0002284336,0.0003344879,0.001306607,0.00183525,0.5901254,0.02072589,0.163361,0.006031837,0.0002673653],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9263169,0.0007628042,0.07108033,0.0001653935,0.00001493463,0.000027757,0.0006983875,0.000184403,0.0007490993],"genre_scores_gemma":[0.9293809,0.0002886121,0.06801002,0.00004917987,0.00002198391,0.00002393421,0.001962059,0.0001360091,0.0001273535],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.006027754,"threshold_uncertainty_score":0.03187823,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01291836166448507,"score_gpt":0.2321676842736921,"score_spread":0.219249322609207,"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."}}