{"id":"W2111939425","doi":"10.1101/gr.3033805","title":"Prokaryotic phylogenies inferred from protein structural domains","year":2005,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":41,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"National Institutes of Health; Howard Hughes Medical Institute","keywords":"Phylogenetic tree; Biology; Phylogenetics; Evolutionary biology; Phylogenetic network; Computational phylogenetics; Sequence (biology); Genome; Computational biology; Gene; Genetics","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":[0.0003678288,0.0001804628,0.000173248,0.0000898659,0.0003015096,0.00006311377,0.0004088999,0.0001319263,0.0001139098],"category_scores_gemma":[0.00009300639,0.0001626553,0.00008548186,0.0001540145,0.0002444765,0.000001095775,0.000474051,0.000207346,0.00009271834],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004493449,"about_ca_system_score_gemma":0.0001355438,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001141176,"about_ca_topic_score_gemma":0.0002110847,"domain_scores_codex":[0.9981786,0.000152187,0.000220406,0.0004986688,0.0003342047,0.0006159262],"domain_scores_gemma":[0.999078,0.0000232498,0.00003968561,0.0005240213,0.0002013392,0.0001336593],"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":[0.00007343569,0.00002624159,0.003022298,0.00001048237,0.0001057943,0.000002940256,0.0002405877,0.00009920065,0.9925783,0.000114152,0.0002080154,0.003518594],"study_design_scores_gemma":[0.001809916,0.0009596043,0.2321231,0.00001971358,0.0000257408,0.00001669348,0.0005825245,0.0001737977,0.4467951,0.004579019,0.312072,0.0008427353],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9921176,0.004857956,0.00003979606,0.0004722474,0.00005500534,0.0005919342,0.0001450245,0.000005157732,0.001715297],"genre_scores_gemma":[0.9942514,0.0002040586,0.00275673,0.00005844482,0.00110264,0.0001223594,0.0001135857,0.00003239106,0.001358345],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5457831,"threshold_uncertainty_score":0.6632891,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03705760264061906,"score_gpt":0.3228592788532892,"score_spread":0.2858016762126702,"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."}}