{"id":"W2137076742","doi":"10.1080/10635150801910436","title":"Testing Congruence in Phylogenomic Analysis","year":2008,"lang":"en","type":"article","venue":"Systematic Biology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":204,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; University of Auckland; Canadian Institute for Advanced Research; Alfred P. Sloan Foundation; Nova Scotia Health Research Foundation; Allan Wilson Centre","keywords":"Biology; Phylogenetic tree; Phylogenetics; Phylogenomics; Evolutionary biology; Eukaryote; Genome; Congruence (geometry); Phylogenetic network; Set (abstract data type); Tree (set theory); Phylogenetic comparative methods; Computational biology; Gene; Genetics; Clade; Computer science; Mathematics","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":[0.04718261,0.001464829,0.002243527,0.006708317,0.002322257,0.004009105,0.002574916,0.001567811,0.002375959],"category_scores_gemma":[0.1839802,0.0007967314,0.002551028,0.006558854,0.005116047,0.002835613,0.005144929,0.003165724,0.0006054268],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009743004,"about_ca_system_score_gemma":0.001358626,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0009859659,"about_ca_topic_score_gemma":0.0008551339,"domain_scores_codex":[0.9198015,0.04936862,0.007314933,0.01165572,0.009453713,0.002405542],"domain_scores_gemma":[0.8245046,0.1410087,0.009634608,0.01445136,0.007346244,0.003054483],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.005239865,0.0006181513,0.7333135,0.001544069,0.005810958,0.003672679,0.00686313,0.0327046,0.06893914,0.03026763,0.002483829,0.1085424],"study_design_scores_gemma":[0.0007165995,0.003075909,0.3453327,0.0003377917,0.001703313,0.003195345,0.006835719,0.4655882,0.0406376,0.1229905,0.009226339,0.0003600647],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7685872,0.0005831865,0.2228895,0.0004463804,0.0001327965,0.0004251041,0.001404551,0.0006037472,0.004927612],"genre_scores_gemma":[0.9265079,0.00007140553,0.07080983,0.0001517013,0.00004969991,0.0003141953,0.001792591,0.0001664858,0.0001362151],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04718261,"threshold_uncertainty_score":0.2495285,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02614091104567686,"score_gpt":0.2501323611668033,"score_spread":0.2239914501211265,"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."}}