{"id":"W2982255935","doi":"10.1093/molbev/msz240","title":"Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data","year":2019,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":716,"is_retracted":false,"has_abstract":true,"ca_institutions":"AIDS Vancouver","funders":"National Institute of Allergy and Infectious Diseases; Shenzhen Peacock Plan; National Institutes of Health; Southern Medical University; National Natural Science Foundation of China","keywords":"Biology; Phylogenetic tree; Tree (set theory); Evolutionary biology; R package; Phylogenetics; Computational biology; Genetics; Gene; Computer science; Programming language; Combinatorics","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.007675185,0.003757564,0.00370386,0.005502277,0.001471436,0.005120101,0.005897596,0.001971318,0.115908],"category_scores_gemma":[0.03948531,0.003075532,0.003906066,0.005050889,0.001475933,0.005395306,0.005440919,0.005527325,0.1050058],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001054729,"about_ca_system_score_gemma":0.004254442,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003581827,"about_ca_topic_score_gemma":0.004846217,"domain_scores_codex":[0.9939663,0.002307703,0.0006231507,0.001513183,0.001202764,0.0003869096],"domain_scores_gemma":[0.9833123,0.009908628,0.001962389,0.002150831,0.002101935,0.0005638324],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0005194421,0.00005294708,0.003182705,0.005276398,0.001099713,0.0003903812,0.0005432124,0.003928551,0.003760832,0.009133973,0.9237704,0.04834139],"study_design_scores_gemma":[0.0003653703,0.00009361976,0.004449091,0.001187224,0.0005310901,0.0008563952,0.0001856486,0.01978683,0.006068152,0.04934352,0.9167611,0.0003720073],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.002385166,0.001535867,0.3425281,0.0009589549,0.0009218574,0.0004769379,0.2585182,0.3843375,0.008337445],"genre_scores_gemma":[0.01606368,0.001441034,0.4001749,0.001397891,0.0003877388,0.003041992,0.234634,0.3331727,0.009686128],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.115908,"threshold_uncertainty_score":0.3877509,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01166612414249821,"score_gpt":0.2503311725949783,"score_spread":0.2386650484524801,"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."}}