{"id":"W3021922824","doi":"10.1073/pnas.2007062117","title":"Median-joining network analysis of SARS-CoV-2 genomes is neither phylogenetic nor evolutionary","year":2020,"lang":"en","type":"letter","venue":"Proceedings of the National Academy of Sciences","topic":"Evolution and Genetic Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":64,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto; Royal Ontario Museum","funders":"","keywords":"Phylogenetic tree; Coronavirus disease 2019 (COVID-19); Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); 2019-20 coronavirus outbreak; Biology; Genome; Genetics; Virology; Gene; Medicine","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004224718,0.0002120083,0.0004121808,0.0002501956,0.0001270069,0.0000129211,0.001149105,0.0004289562,0.00001903393],"category_scores_gemma":[0.0001800041,0.0001661652,0.0003842656,0.001467609,0.0009958397,0.00000947231,0.0003134425,0.0003412073,0.000001365534],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002289544,"about_ca_system_score_gemma":0.0001163695,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000005579945,"about_ca_topic_score_gemma":4.114734e-7,"domain_scores_codex":[0.9975488,0.00001869214,0.0005644282,0.0004974795,0.001120087,0.0002505112],"domain_scores_gemma":[0.9985245,0.00004587911,0.0009589443,0.00002905866,0.0004144255,0.00002711858],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00002240063,0.00002366343,0.007596006,0.0001340502,0.0008414353,3.245747e-8,0.00009333147,0.002322835,0.4376023,0.0003218213,0.5509123,0.0001298482],"study_design_scores_gemma":[0.0009948649,0.0007377614,0.1597143,0.0004050343,0.003206938,0.00002919791,0.0002533343,0.06309567,0.3941715,0.03070756,0.3449681,0.001715718],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"commentary","genre_gemma":"empirical","genre_scores_codex":[0.3146695,0.009854455,0.0001149808,0.6625606,0.0002438148,0.0009969212,0.001395561,0.00002802727,0.01013614],"genre_scores_gemma":[0.7554708,0.0006366044,0.006506352,0.2349974,0.001668473,0.00002001448,0.00004120114,0.00002846752,0.0006307255],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.4408013,"threshold_uncertainty_score":0.6776022,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03740245139193187,"score_gpt":0.3014169241371893,"score_spread":0.2640144727452574,"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."}}