{"id":"W2580191062","doi":"10.1093/sysbio/syw105","title":"Phylogenomics from Whole Genome Sequences Using aTRAM","year":2016,"lang":"en","type":"article","venue":"Systematic Biology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":79,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"","keywords":"Phylogenomics; Genome; Coalescent theory; Biology; Phylogenetic tree; Computational biology; Gene; Tree (set theory); Phylogenetics; Genomics; Genetics; Evolutionary biology; Clade","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002156058,0.001644859,0.001923234,0.005515367,0.001307364,0.002579102,0.001884194,0.001243058,0.005374151],"category_scores_gemma":[0.005650679,0.001435847,0.003360671,0.006263577,0.0004430723,0.00223953,0.002029706,0.003224931,0.00412696],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000628182,"about_ca_system_score_gemma":0.000909014,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006223281,"about_ca_topic_score_gemma":0.0008031187,"domain_scores_codex":[0.998811,0.0002631928,0.0001635508,0.0004546097,0.0002351058,0.00007239864],"domain_scores_gemma":[0.9987258,0.0004878672,0.0002765908,0.0002688891,0.0001809171,0.00005990031],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.002700225,0.0005649608,0.01040023,0.008343514,0.002765791,0.002477233,0.002845551,0.02169673,0.6094896,0.02061669,0.02587466,0.2922249],"study_design_scores_gemma":[0.0004442561,0.001003887,0.02695835,0.0009472703,0.001592192,0.002252004,0.001020064,0.4289283,0.2718979,0.04445778,0.2200238,0.0004741678],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.07380288,0.002259274,0.8267242,0.000520498,0.0004333871,0.000345422,0.02639115,0.06528004,0.004243155],"genre_scores_gemma":[0.1255882,0.001912821,0.8024077,0.0002400189,0.0001478338,0.001080926,0.06075167,0.006762055,0.001108927],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.005515367,"threshold_uncertainty_score":0.01797837,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0240217731885108,"score_gpt":0.2525460667467729,"score_spread":0.2285242935582621,"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."}}