{"id":"W3199649297","doi":"10.1099/ijsem.0.005011","title":"Phylogenomic and comparative genomic analyses of species of the family Pseudomonadaceae: Proposals for the genera Halopseudomonas gen. nov. and Atopomonas gen. nov., merger of the genus Oblitimonas with the genus Thiopseudomonas, and transfer of some misclassified species of the genus Pseudomonas into other genera","year":2021,"lang":"en","type":"article","venue":"INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":62,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University","funders":"Ontario Ministry of Research, Innovation and Science; Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada","keywords":"Biology; Clade; Phylogenetic tree; Phylogenetics; Genus; Type genus; Clostridiales; Zoology; Type species; Genetics; 16S ribosomal RNA; Bacteria; Gene","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":[0.0006062409,0.000332291,0.0009255431,0.00008138597,0.0002394363,0.00001935636,0.000722334,0.000158483,0.000007325713],"category_scores_gemma":[0.00008223877,0.0001523115,0.0003663703,0.0001416134,0.002204232,0.00001153911,0.0004020565,0.0001659134,1.075619e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003884091,"about_ca_system_score_gemma":0.0003647964,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001341756,"about_ca_topic_score_gemma":0.0001370832,"domain_scores_codex":[0.9974306,0.0004705971,0.001258879,0.000326808,0.0002921018,0.0002210321],"domain_scores_gemma":[0.9968577,0.0004158169,0.001215096,0.0004481217,0.001017796,0.00004544522],"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":[0.0003456999,0.00009864518,0.0105549,0.0007728434,0.002674989,0.000001562788,0.001603887,0.0005671199,0.9811156,0.001942198,0.0002775001,0.00004507639],"study_design_scores_gemma":[0.003586647,0.0007230439,0.2164677,0.001169652,0.001859152,0.001965904,0.009459074,0.0004001658,0.7595985,0.001118838,0.003135656,0.0005156825],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9289043,0.06798682,0.0002958929,0.001081678,0.000326531,0.0007837231,0.000578102,7.885941e-7,0.00004217725],"genre_scores_gemma":[0.9955313,0.003176421,0.0007120265,0.0001371436,0.0001738933,0.00002694773,0.000009272736,0.00002112364,0.0002119006],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2215171,"threshold_uncertainty_score":0.8121585,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03782370812911763,"score_gpt":0.2585855421894954,"score_spread":0.2207618340603778,"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."}}