{"id":"W2130138427","doi":"10.1186/s12859-015-0791-x","title":"The Gap Procedure: for the identification of phylogenetic clusters in HIV-1 sequence data","year":2015,"lang":"en","type":"article","venue":"BMC Bioinformatics","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":21,"is_retracted":false,"has_abstract":true,"ca_institutions":"Jewish General Hospital; Centre Hospitalier de l’Université de Montréal; McGill University","funders":"Canadian Institutes of Health Research","keywords":"Phylogenetic tree; Computational biology; Identification (biology); Sequence (biology); Human immunodeficiency virus (HIV); Biology; DNA microarray; Evolutionary biology; Genetics; Virology; Gene","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.007601649,0.001370508,0.001296077,0.00451061,0.001595931,0.001759845,0.002149859,0.002203463,0.00646093],"category_scores_gemma":[0.03369616,0.000788483,0.001492665,0.003677136,0.001430757,0.001921696,0.002649351,0.002473088,0.00393749],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006871386,"about_ca_system_score_gemma":0.002683834,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001528479,"about_ca_topic_score_gemma":0.002217477,"domain_scores_codex":[0.9953447,0.002390282,0.0002421837,0.0007439094,0.0010855,0.0001934617],"domain_scores_gemma":[0.9913936,0.005330965,0.0007181668,0.001282422,0.0009995288,0.000275276],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001147865,0.0002941939,0.0145893,0.001639403,0.0008007589,0.0006992155,0.00169053,0.05265365,0.01898741,0.04037075,0.02851587,0.8386111],"study_design_scores_gemma":[0.0003069368,0.0004309193,0.009427142,0.0002939994,0.0001810645,0.001633599,0.0005753139,0.8478205,0.01747286,0.08478596,0.03691532,0.0001563805],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.009546707,0.0002002436,0.9834061,0.0001135695,0.00004814764,0.0003092735,0.0007637005,0.005129121,0.0004832929],"genre_scores_gemma":[0.02630654,0.0000732195,0.9710192,0.00005320091,0.00002119524,0.0004379074,0.00117458,0.0006152843,0.0002987659],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.007601649,"threshold_uncertainty_score":0.04020184,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1324022032828855,"score_gpt":0.3364065460040913,"score_spread":0.2040043427212058,"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."}}