{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001749972,0.0001158287,0.0001435923,0.00007092216,0.00005464155,0.000003383252,0.00008565793,0.0001844377,0.000002372386],"category_scores_gemma":[0.0001185949,0.0001116791,0.00004636738,0.00007699195,0.0002122944,0.000001094867,0.00009824184,0.00009424428,9.493198e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000005891277,"about_ca_system_score_gemma":0.00004696496,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001131962,"about_ca_topic_score_gemma":0.0004437172,"domain_scores_codex":[0.9992458,0.00005785488,0.0002010379,0.0002684236,0.00003697757,0.0001898983],"domain_scores_gemma":[0.9996569,0.0000133787,0.0000728118,0.0001646185,0.00005531154,0.00003703074],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0000267637,0.00003060033,0.2838945,0.000007097106,0.00001969583,0.000001197138,0.0000118543,0.0001985169,0.71417,0.001309272,0.000008762442,0.0003217699],"study_design_scores_gemma":[0.0005187304,0.000358087,0.8527226,0.00001031962,0.00001852026,0.00003485963,0.00002784187,0.0005113392,0.1385413,0.006721932,0.0003531992,0.0001813034],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9934632,0.002928149,0.003035922,0.00007475782,0.0001100442,0.0001531062,0.00001497133,0.00000268397,0.0002171759],"genre_scores_gemma":[0.9967788,0.0000763772,0.002935297,0.00003445521,0.00006350007,0.00002352582,0.00004415918,0.000009133358,0.00003475621],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5756287,"threshold_uncertainty_score":0.4554141,"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."}}