{"id":"W2980963357","doi":"10.1099/ijsem.0.003775","title":"A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov.","year":2019,"lang":"en","type":"article","venue":"INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY","topic":"Bacillus and Francisella bacterial research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":303,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Biology; Polyphyly; Genus; Taxonomy (biology); Evolutionary biology; Zoology; Phylogenetics; Genetics; Gene; 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":["metaepi_narrow"],"consensus_categories":["metaepi_narrow"],"category_scores_codex":[0.002768564,0.001476515,0.003044471,0.0006127887,0.0007780769,0.0002685179,0.002489815,0.001189967,0.0002023747],"category_scores_gemma":[0.001066234,0.001060622,0.001304406,0.0005318475,0.002076457,0.0001594326,0.001500317,0.0009597883,0.00003124976],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006785006,"about_ca_system_score_gemma":0.00193147,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003160411,"about_ca_topic_score_gemma":0.0002999439,"domain_scores_codex":[0.9907339,0.0009444013,0.003921648,0.001725078,0.001074924,0.001600028],"domain_scores_gemma":[0.9904156,0.001044058,0.003376804,0.001456866,0.003099398,0.0006073269],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.004167093,0.0003886307,0.001939112,0.003369572,0.004675412,0.00002735928,0.002538615,0.0009181657,0.9729837,0.005348119,0.002129225,0.001514999],"study_design_scores_gemma":[0.09696858,0.03135946,0.06158506,0.01857733,0.0115808,0.05860486,0.03210909,0.02112137,0.218279,0.01269548,0.419057,0.01806198],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9157409,0.05263856,0.0149843,0.001586935,0.004023554,0.005504129,0.005192121,0.00002871617,0.0003007611],"genre_scores_gemma":[0.9777064,0.003541986,0.01356927,0.0004341265,0.002302011,0.0001885358,0.0004277464,0.0001610904,0.001668778],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7547047,"threshold_uncertainty_score":0.9997984,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02717076120021597,"score_gpt":0.263950560448846,"score_spread":0.23677979924863,"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."}}