{"id":"W2115171147","doi":"10.1093/molbev/msp289","title":"Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1","year":2009,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":66,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University; AIDS Vancouver","funders":"National Institute of Mental Health; National Institute of Allergy and Infectious Diseases; Canadian Institutes of Health Research","keywords":"Biology; Nonsynonymous substitution; Phylogenetic tree; Genetics; Population; Phylogenetics; Evolutionary biology; Gene; Genome","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003036505,0.0000708692,0.0001870154,0.0002598788,0.00005995951,0.000003349225,0.0001273756,0.00009655571,0.00001186025],"category_scores_gemma":[0.0001076225,0.00005292025,0.00002862185,0.0003307757,0.000083151,0.00002003933,0.0000424866,0.00006229663,0.000003200082],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002277551,"about_ca_system_score_gemma":0.00001997716,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0004778681,"about_ca_topic_score_gemma":0.0003418644,"domain_scores_codex":[0.9991705,0.0002728401,0.0001764083,0.0002098742,0.00002241695,0.0001479301],"domain_scores_gemma":[0.9995452,0.0000861532,0.0000556232,0.0002696381,0.0000304892,0.00001294462],"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":[0.00003462724,0.0000303332,0.3526759,0.000004125751,0.0001359049,0.000002066304,0.00008692304,0.0003710058,0.6456609,0.0001727017,0.000005113717,0.0008204098],"study_design_scores_gemma":[0.0003554401,0.0001885056,0.9873207,0.000007414761,0.0001934549,0.000004096905,0.00006484544,0.001266472,0.01026847,0.0002728148,0.000008127075,0.00004966727],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9857544,0.006217458,0.007563736,0.0001885011,0.000009722476,0.000141029,0.000112064,0.000003508437,0.000009575565],"genre_scores_gemma":[0.9974556,0.00003503965,0.0004770842,0.00006853746,0.0000022838,0.000004104883,0.001953181,0.000001750898,0.000002442953],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6353924,"threshold_uncertainty_score":0.2158025,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02390683473631989,"score_gpt":0.3192152349149137,"score_spread":0.2953084001785938,"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."}}