{"id":"W2152570956","doi":"10.1093/molbev/msq323","title":"Harvesting Evolutionary Signals in a Forest of Prokaryotic Gene Trees","year":2010,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":37,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal","funders":"Natural Sciences and Engineering Research Council of Canada; Muséum National d'Histoire Naturelle","keywords":"Biology; Phylogenetic tree; Archaea; Horizontal gene transfer; Phylogenetics; Tree of life (biology); Evolutionary biology; Phylogenetic network; Phylogenomics; Gene; Genome; Gene duplication; 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":[0.0004584521,0.0002768114,0.0003356996,0.001439518,0.0004898721,0.000872105,0.0003224172,0.0003068861,0.000739636],"category_scores_gemma":[0.002349993,0.0004045185,0.0004560596,0.001361639,0.0007321119,0.001104912,0.0006077706,0.0007096519,0.0002042388],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003191032,"about_ca_system_score_gemma":0.0002896741,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001505921,"about_ca_topic_score_gemma":0.002910789,"domain_scores_codex":[0.9998155,0.00003999755,0.00001079168,0.00005701347,0.00003942393,0.00003714437],"domain_scores_gemma":[0.9990201,0.0005513309,0.0001269504,0.0001121291,0.0001053581,0.00008403161],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.001006736,0.0001753952,0.1477541,0.0009487101,0.0003286308,0.002300649,0.005553368,0.1304991,0.4913082,0.02989637,0.002166842,0.1880619],"study_design_scores_gemma":[0.0000478482,0.0002989004,0.2501988,0.0002509193,0.0002857979,0.002006749,0.003074074,0.5913843,0.06261405,0.07600595,0.01365905,0.0001734932],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8955936,0.000656508,0.1016045,0.0001329423,0.00002346696,0.00002183069,0.0006324625,0.0002474242,0.001087297],"genre_scores_gemma":[0.8961546,0.0004922963,0.1011294,0.00005946209,0.00002583993,0.00003546941,0.001667349,0.000155109,0.0002804905],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001505921,"threshold_uncertainty_score":0.002994299,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006194895874093131,"score_gpt":0.2354474515230634,"score_spread":0.2292525556489702,"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."}}