{"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":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0004483541,0.000313619,0.0004154609,0.00005554616,0.0004443826,0.0001221803,0.0008540373,0.0002490085,0.00001881177],"category_scores_gemma":[0.0001128175,0.0003067766,0.00006226328,0.00004982756,0.0002254892,0.00001113971,0.0009361201,0.0001664715,0.000002702276],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007527859,"about_ca_system_score_gemma":0.0003530954,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001436811,"about_ca_topic_score_gemma":0.001157605,"domain_scores_codex":[0.9981255,0.00009594905,0.0004317957,0.0007784964,0.0001462849,0.000422002],"domain_scores_gemma":[0.9979021,0.00002562177,0.0003229456,0.001480156,0.0001368458,0.0001323511],"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":[0.00004758159,0.0000154118,0.05292774,0.00003469651,0.0001499657,0.000008182667,0.0001934592,0.0001480054,0.9457372,0.00001571341,0.00001201807,0.0007100339],"study_design_scores_gemma":[0.003702016,0.000936616,0.3540532,0.0004027567,0.001182539,0.0006034403,0.002141936,0.006154058,0.5910779,0.002463863,0.03363251,0.003649224],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9941301,0.001797241,0.00145594,0.00006310587,0.0002190441,0.0002504534,0.001353055,0.000007187275,0.0007238942],"genre_scores_gemma":[0.9922286,0.00167648,0.005192237,0.00007248708,0.0004042064,0.0000112893,0.0003327994,0.00003310442,0.00004883486],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3546593,"threshold_uncertainty_score":0.9999384,"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."}}