{"id":"W2143794041","doi":"10.1093/sysbio/syu023","title":"Supertrees Based on the Subtree Prune-and-Regraft Distance","year":2014,"lang":"en","type":"article","venue":"Systematic Biology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":90,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University","funders":"Killam Trusts; Natural Sciences and Engineering Research Council of Canada; Canada Research Chairs","keywords":"Supertree; Biology; Phylogenomics; Phylogenetic tree; Maximum parsimony; Phylum; Phylogenetics; Horizontal gene transfer; Tree (set theory); Supermatrix; Benchmark (surveying); Evolutionary biology; Tree of life (biology); Computational biology; Gene; Mathematics; Genetics; Combinatorics; Clade","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004615711,0.0001572005,0.000257288,0.00002157004,0.0001142923,0.00001625925,0.0001982859,0.000102506,0.000004670016],"category_scores_gemma":[0.0003064833,0.00008684886,0.00006838627,0.00003721371,0.0001646549,1.960804e-7,0.00008827155,0.00005242185,0.000008989461],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000004702183,"about_ca_system_score_gemma":0.00001494383,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000009842377,"about_ca_topic_score_gemma":0.00006986191,"domain_scores_codex":[0.9989544,0.0002962976,0.0002263107,0.0002796861,0.00005159223,0.0001917857],"domain_scores_gemma":[0.9991634,0.0001807909,0.00008583501,0.0004919232,0.00004038736,0.0000376342],"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":[0.0001540621,0.0001684974,0.1700062,0.006660895,0.0004960039,0.000002314179,0.0003767378,0.0002715324,0.6791509,0.1410448,0.001061392,0.0006066589],"study_design_scores_gemma":[0.01318558,0.01761368,0.3772851,0.01015131,0.001471326,0.0002943929,0.004716669,0.1094123,0.3220792,0.07011184,0.06551432,0.008164256],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9895941,0.001568067,0.005219553,0.001369875,0.0001750242,0.000503451,0.00001363732,0.000006321942,0.001549971],"genre_scores_gemma":[0.998664,0.00002500415,0.000214242,0.0007875739,0.0000929872,0.0001235747,0.000008660366,0.00001150787,0.00007247734],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3570717,"threshold_uncertainty_score":0.3541594,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009303417958051773,"score_gpt":0.2117532545432933,"score_spread":0.2024498365852415,"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."}}