{"id":"W2597711052","doi":"10.1139/gen-2016-0202","title":"Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (<i>Quercus</i> section <i>Quercus</i>)","year":2017,"lang":"en","type":"article","venue":"Genome","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":58,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Science Foundation","keywords":"Biology; Phylogenetic tree; Sequence assembly; DNA sequencing; Phylogenetics; Genome; Evolutionary biology; Clade; Computational biology; Phylogenomics; Reference genome; Genetics; Gene","routes":{"ca_aff":false,"ca_fund":false,"ca_venue":true,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001187648,0.0004485036,0.0003413465,0.0007156401,0.0004562411,0.001220726,0.0003442427,0.0002997461,0.0004684417],"category_scores_gemma":[0.00192647,0.0003303668,0.0004878336,0.000550855,0.0002953905,0.0004146834,0.0003035774,0.0006458816,0.000237813],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007947289,"about_ca_system_score_gemma":0.0006578483,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.006250795,"about_ca_topic_score_gemma":0.009922327,"domain_scores_codex":[0.9995914,0.00007684024,0.00003122239,0.0001879177,0.00007441597,0.00003813922],"domain_scores_gemma":[0.9995334,0.0001906096,0.00007233296,0.00006757468,0.0000926735,0.00004344891],"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":[0.001385616,0.0002112364,0.1610527,0.00031447,0.0002340824,0.0004494039,0.001401021,0.02574094,0.7562448,0.002576246,0.0004997835,0.04988965],"study_design_scores_gemma":[0.0001130133,0.0005368594,0.6816492,0.0001450298,0.0005541483,0.0006216897,0.001284556,0.1047552,0.1910144,0.004771954,0.01441064,0.0001433515],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9750279,0.0004050967,0.02178692,0.00004276839,0.00001398088,0.00002991826,0.001293063,0.0001787139,0.001221557],"genre_scores_gemma":[0.9399101,0.0004579957,0.05086466,0.00007320967,0.00001186385,0.00003588255,0.007665248,0.0001573775,0.0008236215],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.006250795,"threshold_uncertainty_score":0.01242882,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1040500452462459,"score_gpt":0.3125927886891783,"score_spread":0.2085427434429324,"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."}}