{"id":"W2952123522","doi":"10.1093/nar/gkz246","title":"AnnoTree: visualization and exploration of a functionally annotated microbial tree of life","year":2019,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":351,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Waterloo","funders":"Australian Research Council; Natural Sciences and Engineering Research Council of Canada","keywords":"Biology; Horizontal gene transfer; Phylogenetic tree; Tree of life (biology); Genome; Bacterial genome size; Phylogenetics; Gene; Evolutionary biology; Lineage (genetic); Annotation; Computational biology; Phylogenomics; Genomics; Metagenomics; Comparative genomics; Genetics; Clade","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":[0.001355581,0.001389801,0.0009852814,0.003391524,0.000916343,0.002448041,0.001602622,0.001110654,0.02220146],"category_scores_gemma":[0.002819978,0.0007032325,0.001202667,0.002337407,0.0003673643,0.00271944,0.003206797,0.001594497,0.004193039],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006644147,"about_ca_system_score_gemma":0.001107591,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003854426,"about_ca_topic_score_gemma":0.006879437,"domain_scores_codex":[0.9995783,0.0001044755,0.00003146524,0.00009225553,0.0001253429,0.00006817259],"domain_scores_gemma":[0.9986024,0.0006427701,0.0001215869,0.000173726,0.0002408474,0.0002186496],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.002988227,0.0004454926,0.0181153,0.005281199,0.0007712935,0.00201974,0.005536209,0.01674113,0.1292787,0.02874802,0.4836933,0.3063814],"study_design_scores_gemma":[0.0004955711,0.0002871553,0.01929877,0.001159856,0.0002543557,0.001981713,0.001735203,0.2393762,0.05224163,0.04262452,0.6399912,0.0005538859],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.06871355,0.002822099,0.4904969,0.002424455,0.0006402396,0.0002482068,0.1025863,0.3151773,0.01689097],"genre_scores_gemma":[0.2816143,0.003839865,0.5392624,0.0009246231,0.0002235056,0.0008409497,0.1249653,0.04014524,0.008183683],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.02220146,"threshold_uncertainty_score":0.07427126,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04055615777622439,"score_gpt":0.3141428850664184,"score_spread":0.273586727290194,"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."}}