{"id":"W2953324593","doi":"10.1093/sysbio/syx058","title":"Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics","year":2017,"lang":"en","type":"article","venue":"Systematic Biology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":62,"is_retracted":false,"has_abstract":true,"ca_institutions":"Royal Ontario Museum; University of Toronto","funders":"","keywords":"Biology; Phylogenetic tree; Phylogenomics; Evolutionary biology; Coalescent theory; Clade; Phylogenetics; Indel; Supermatrix; Genetics; Gene","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":[0.0005473718,0.000170607,0.0004851428,0.00002820268,0.0001776245,0.00001990391,0.000464069,0.0001754385,0.000003391421],"category_scores_gemma":[0.0004114393,0.0001411204,0.0001715902,0.00001221412,0.0002160009,5.517232e-7,0.0002980412,0.00003537484,0.000002484823],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001063695,"about_ca_system_score_gemma":0.00006652385,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002315344,"about_ca_topic_score_gemma":0.00005877004,"domain_scores_codex":[0.9987883,0.00005808535,0.0005516414,0.0003075778,0.00003997635,0.000254419],"domain_scores_gemma":[0.9982392,0.00005373247,0.0006473155,0.0008511176,0.0001670931,0.00004158351],"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":[0.00007355283,0.0000546154,0.02724546,0.003298574,0.0004766459,1.547841e-7,0.00003797794,0.000005918003,0.9662016,0.002513826,0.00004826903,0.00004341662],"study_design_scores_gemma":[0.02366453,0.006679296,0.2031778,0.003689306,0.001774142,0.0001509696,0.00225347,0.006606214,0.7208982,0.01555084,0.01206772,0.00348755],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9911428,0.001237831,0.005350253,0.0001288374,0.0003738508,0.001131301,0.0001942177,0.000002243219,0.0004386334],"genre_scores_gemma":[0.9948603,0.00005476639,0.004491912,0.00009663153,0.00009987351,0.0002409922,0.00002941536,0.00001789396,0.0001082251],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2453034,"threshold_uncertainty_score":0.5754723,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03237466006196306,"score_gpt":0.2866234409762973,"score_spread":0.2542487809143342,"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."}}