{"id":"W4283722976","doi":"10.3390/microorganisms10071312","title":"Phylogenomic Analyses and Molecular Signatures Elucidating the Evolutionary Relationships amongst the Chlorobia and Ignavibacteria Species: Robust Demarcation of Two Family-Level Clades within the Order Chlorobiales and Proposal for the Family Chloroherpetonaceae fam. nov","year":2022,"lang":"en","type":"article","venue":"Microorganisms","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":11,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Guelph; McMaster University","funders":"Natural Sciences and Engineering Research Council of Canada; Ontario Ministry of Research, Innovation and Science","keywords":"Clade; Biology; Monophyly; Candidatus; Evolutionary biology; Phylogenomics; Phylogenetic tree; Phylogenetics; Indel; Genetics; Genome; 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":["sts"],"consensus_categories":[],"category_scores_codex":[0.0006923721,0.000239564,0.0001919364,0.00003002163,0.001806302,0.00008604266,0.0003705679,0.0000736349,0.000004514986],"category_scores_gemma":[0.00009881797,0.0001292102,0.00006698909,0.0001623147,0.000727892,0.000004351482,0.000546108,0.0002390602,2.316711e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002149573,"about_ca_system_score_gemma":0.0001456903,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000135876,"about_ca_topic_score_gemma":0.0001795014,"domain_scores_codex":[0.998694,0.000228344,0.0003302679,0.000390427,0.0001395355,0.0002174419],"domain_scores_gemma":[0.998917,0.0002608662,0.0002657802,0.0003903073,0.0001366389,0.00002936054],"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":[0.00006851527,0.00002170549,0.001768413,0.00001819992,0.0002280661,3.296502e-7,0.00141799,0.002290358,0.99235,0.00136167,0.0003350822,0.000139701],"study_design_scores_gemma":[0.001556496,0.0004839683,0.5150153,0.00002842765,0.0006770101,0.000102682,0.03272563,0.001462757,0.4377573,0.00407145,0.005457592,0.0006613672],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9780281,0.01701135,0.001942167,0.001629382,0.0001202857,0.0009291146,0.0003058424,0.000004566423,0.0000292025],"genre_scores_gemma":[0.9958435,0.0004978044,0.002744254,0.0004155753,0.0001265342,0.0001201884,0.0001192201,0.00003620812,0.00009677336],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5545927,"threshold_uncertainty_score":0.9994932,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04315563137276097,"score_gpt":0.2586880286443712,"score_spread":0.2155323972716102,"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."}}