{"id":"W3216525517","doi":"10.1093/ve/veab092","title":"CoVizu: Rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes","year":2021,"lang":"en","type":"article","venue":"Virus Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":13,"is_retracted":false,"has_abstract":true,"ca_institutions":"Western University","funders":"","keywords":"Genome; Indel; Phylogenetic tree; Lineage (genetic); Biology; Computational biology; Bacterial genome size; Comparative genomics; Genomics; 1000 Genomes Project; Python (programming language); Phylogenetics; Synteny; Evolutionary biology; Coalescent theory; Genetics; Computer science; Gene; Single-nucleotide polymorphism","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":[0.00005942129,0.00005160537,0.0001036861,0.00001745964,0.00008180244,0.00000263076,0.00005951416,0.00004663118,0.000002242418],"category_scores_gemma":[0.00002507075,0.00004412704,0.00008471827,0.0002521688,0.00007692062,5.286805e-7,0.0002938036,0.00001058738,1.82114e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000146962,"about_ca_system_score_gemma":0.00003298973,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002402622,"about_ca_topic_score_gemma":0.0006225561,"domain_scores_codex":[0.9995875,0.00004723387,0.000105998,0.0001300036,0.00006931093,0.00005996448],"domain_scores_gemma":[0.9996352,0.000003475503,0.00008526685,0.0001533464,0.0001136829,0.000008980741],"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":[0.00001269135,0.00001894219,0.3298386,0.000007805034,0.0002133344,6.736018e-8,0.0000361438,0.00004772411,0.6692023,0.0002941176,0.00003668235,0.0002915724],"study_design_scores_gemma":[0.0001198129,0.00003006851,0.5199715,0.00000152887,0.0001774869,7.30815e-7,0.00003505859,0.00008294083,0.4788231,0.0002301024,0.0004894054,0.00003823029],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.992186,0.004707269,0.002675457,0.00001947087,0.00005006825,0.00004297587,0.00008557225,7.676619e-7,0.0002324092],"genre_scores_gemma":[0.9990762,0.0007320346,0.0001096149,0.00003278382,0.00001684882,7.226396e-7,0.00001739717,0.000001896062,0.00001248039],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1903792,"threshold_uncertainty_score":0.1799448,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01703483866833012,"score_gpt":0.2604323085630957,"score_spread":0.2433974698947656,"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."}}