{"id":"W4315778117","doi":"10.12938/bmfh.2022-017","title":"Phylogenomic analysis in <i>Latilactobacillus sakei</i> by using polymorphisms detected by next-generation sequencing","year":2023,"lang":"en","type":"article","venue":"Bioscience of Microbiota Food and Health","topic":"Identification and Quantification in Food","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Institute of Genetics; Japan Society for the Promotion of Science; Mitani Foundation for Research and Development; Research Organization of Information and Systems","keywords":"Phylogenetic tree; Biology; Lactobacillus sakei; Genetics; Whole genome sequencing; Locus (genetics); Haplotype; Genome; Computational biology; Gene; Genotype; Bacteria; Lactic acid","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001906997,0.0002569841,0.0002738783,0.0009260314,0.000293644,0.0004223667,0.0001262101,0.000192389,0.0007842328],"category_scores_gemma":[0.0002933818,0.0001026717,0.0003518414,0.0008440498,0.0001421074,0.0001699802,0.0002504691,0.0002652273,0.0003439468],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001543647,"about_ca_system_score_gemma":0.0002183696,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00164131,"about_ca_topic_score_gemma":0.001720193,"domain_scores_codex":[0.9998484,0.00002017653,0.00001571569,0.00005002763,0.00003140263,0.00003436414],"domain_scores_gemma":[0.9998649,0.00002457552,0.00003372956,0.00001233075,0.00004017175,0.00002426626],"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":[0.000167182,0.00003014749,0.01206068,0.00004233482,0.00001971909,0.00007312687,0.0001471401,0.0002038622,0.9806076,0.00007165518,0.00006853176,0.006508016],"study_design_scores_gemma":[0.00002039925,0.000586674,0.5239534,0.00004026548,0.0001948937,0.0009153258,0.0008964784,0.01662625,0.4468332,0.0003190833,0.009580852,0.00003316918],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9894482,0.0003150706,0.006631984,0.00007086063,0.000009832035,0.00003874882,0.002488674,0.00008502627,0.0009116844],"genre_scores_gemma":[0.9717933,0.0003366861,0.01811908,0.00007030209,0.000008382346,0.00008740888,0.008054012,0.00005991087,0.001470872],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.00164131,"threshold_uncertainty_score":0.003263533,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0720813932267545,"score_gpt":0.2887583064801851,"score_spread":0.2166769132534306,"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."}}