{"id":"W3095475495","doi":"10.1099/ijsem.0.004475","title":"Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species","year":2020,"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":515,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University","funders":"","keywords":"Biology; Clade; Phylogenomics; Phylogenetic tree; Monophyly; Phylogenetics; Bacillus (shape); Evolutionary biology; Zoology; Botany; Genetics; Gene","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":[0.0003436241,0.0001729958,0.0005324045,0.00007124976,0.00008772901,0.00001580172,0.0002397916,0.00008820358,0.000004124126],"category_scores_gemma":[0.0001635536,0.0001141461,0.00009960814,0.00006254814,0.000478117,0.000009721639,0.0001851143,0.00006352762,5.599735e-8],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003574068,"about_ca_system_score_gemma":0.00014331,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005491695,"about_ca_topic_score_gemma":0.0001465439,"domain_scores_codex":[0.9985269,0.0001470068,0.0008710238,0.0002218255,0.000114811,0.0001184103],"domain_scores_gemma":[0.9980003,0.0001137098,0.0010183,0.0001218319,0.0006898576,0.00005595781],"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":[0.000403444,0.00005835517,0.007750128,0.0007914621,0.0007481067,2.383286e-7,0.001745025,0.001240692,0.9866349,0.000216595,0.0003804944,0.00003052225],"study_design_scores_gemma":[0.01014348,0.01025657,0.3053116,0.003218338,0.002884887,0.003489352,0.06297997,0.01161015,0.5841057,0.0007100469,0.003786745,0.001503173],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9907085,0.005322993,0.001853192,0.0006785468,0.0001090683,0.0005922302,0.0006956977,6.513719e-7,0.00003907295],"genre_scores_gemma":[0.9950531,0.0004895389,0.004197,0.00005804898,0.00008799779,0.000005717406,0.0000546225,0.000008047081,0.00004593664],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4025293,"threshold_uncertainty_score":0.4654744,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.08682491615456048,"score_gpt":0.2746243076221522,"score_spread":0.1877993914675917,"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."}}