{"id":"W2951211878","doi":"10.1099/mgen.0.000116","title":"SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology","year":2017,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":162,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Centre for Disease Control; Dalhousie University; Simon Fraser University; Health Canada; University of Manitoba; Public Health Agency of Canada","funders":"Genome British Columbia; Genome Canada","keywords":"Phylogenomics; Indel; Computational biology; Genome; Whole genome sequencing; Scalability; Biology; Workflow; Genomics; Pipeline (software); Computer science; Genetics; Data mining; Phylogenetic tree; Single-nucleotide polymorphism; Database; Clade; Gene; Operating system","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":[],"category_scores_codex":[0.0007875525,0.0005631717,0.0007570029,0.00008001075,0.001170739,0.0001502402,0.00128877,0.0004296829,0.00001482827],"category_scores_gemma":[0.0004417949,0.0006149347,0.0005163621,0.00003175254,0.0005104978,0.000003703006,0.0009344007,0.0001815684,0.00005273676],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001245324,"about_ca_system_score_gemma":0.0002831545,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001577033,"about_ca_topic_score_gemma":0.0004499322,"domain_scores_codex":[0.996831,0.0001026247,0.0008547576,0.00112659,0.00005564961,0.001029406],"domain_scores_gemma":[0.9972163,0.0000829787,0.0006885628,0.00156898,0.0002294358,0.00021372],"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":[0.0004547975,0.0001496767,0.0009262675,0.00003442664,0.0002233254,0.000005318168,0.0001091677,0.0002898712,0.9818978,0.0002625105,0.01045902,0.00518783],"study_design_scores_gemma":[0.002922847,0.0005099425,0.003481423,0.00001504163,0.0001650348,0.0001221575,0.00005603892,0.0003131136,0.2256683,0.001151089,0.764563,0.001032007],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9833236,0.001975677,0.008434393,0.001057498,0.002277165,0.001034528,0.001044417,0.00001614643,0.0008366213],"genre_scores_gemma":[0.9660111,0.00103948,0.02407219,0.002085279,0.00438553,0.00007196483,0.0003672338,0.0001937444,0.001773463],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7562295,"threshold_uncertainty_score":0.9996302,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03370385685354935,"score_gpt":0.2675280396315327,"score_spread":0.2338241827779834,"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."}}