{"id":"W2111414304","doi":"10.1371/journal.pbio.1000602","title":"Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough","year":2011,"lang":"en","type":"article","venue":"PLoS Biology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1169,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal","funders":"Natural Environment Research Council; Natural Sciences and Engineering Research Council of Canada; Agence Nationale de la Recherche; Biotechnology and Biological Sciences Research Council; Deutsche Forschungsgemeinschaft","keywords":"Phylogenomics; Biology; Phylogenetic tree; Tree of life (biology); Inference; Evolutionary biology; Phylogenetics; Genome; DNA sequencing; Sequence (biology); Computational biology; Genetics; Gene; Artificial intelligence; Clade; Computer science","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":[],"consensus_categories":[],"category_scores_codex":[0.00009265349,0.0002384574,0.0002495286,0.00004904737,0.0001650091,0.00001118991,0.0003319556,0.000235578,0.00003856401],"category_scores_gemma":[0.0001697337,0.0002027319,0.00008647486,0.00009319253,0.0003080507,8.100005e-7,0.0002204651,0.0000979959,0.00002355317],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001205235,"about_ca_system_score_gemma":0.00004346961,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001167874,"about_ca_topic_score_gemma":0.0001016106,"domain_scores_codex":[0.9986406,0.0001024464,0.0002598652,0.0005432464,0.00006522403,0.0003886294],"domain_scores_gemma":[0.9991742,0.00002250342,0.0001385016,0.0004189198,0.0001622589,0.00008356225],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00005242975,0.0001496093,0.03434424,0.00001594709,0.000168519,0.000004291829,0.000375184,0.00001052559,0.963304,0.000507173,0.0005221734,0.0005458879],"study_design_scores_gemma":[0.000763448,0.001426447,0.2042929,0.00005303291,0.0001385323,0.00005234285,0.0009376865,0.00004293391,0.7483371,0.002173497,0.04084479,0.0009372584],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9929929,0.004702413,0.0001561177,0.0004015524,0.0002207528,0.0002042652,0.00006918786,0.00001538028,0.001237372],"genre_scores_gemma":[0.9933618,0.001124938,0.003933747,0.000962187,0.0003089431,0.00007990453,0.00004871624,0.00002529582,0.0001544377],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2149669,"threshold_uncertainty_score":0.8267166,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04148673099223456,"score_gpt":0.2499117093754345,"score_spread":0.2084249783832,"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."}}