{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002945111,0.0002862345,0.0003744237,0.001169396,0.0005563168,0.000471059,0.000275636,0.0003597967,0.0002832559],"category_scores_gemma":[0.003771223,0.0001978481,0.0003651894,0.001078943,0.0003215668,0.0002065605,0.0004840137,0.0006474461,0.00008965976],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000405724,"about_ca_system_score_gemma":0.0003659446,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001522946,"about_ca_topic_score_gemma":0.00242664,"domain_scores_codex":[0.9991618,0.0003811027,0.00004643052,0.0002259178,0.0001134877,0.00007120327],"domain_scores_gemma":[0.9986613,0.0006763455,0.0002235433,0.0001688082,0.0001451658,0.0001248884],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0005579103,0.0002517326,0.5245676,0.0001712442,0.0009877871,0.0005074766,0.001448769,0.0341722,0.3770629,0.002045834,0.0003699342,0.05785661],"study_design_scores_gemma":[0.0000420278,0.0003926808,0.7382416,0.00004368308,0.0002493368,0.0009217169,0.0008902084,0.2398451,0.01362643,0.002882201,0.002814968,0.00005022055],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9897933,0.0001242429,0.009575393,0.00002521197,0.000002575767,0.00002181149,0.000187757,0.00002142833,0.0002482011],"genre_scores_gemma":[0.9868135,0.00006247844,0.01228944,0.00003114595,0.000003016557,0.00002315087,0.0006995086,0.0000110193,0.00006675711],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002945111,"threshold_uncertainty_score":0.01557541,"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."}}