{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003190948,0.0000680379,0.0001250096,0.00008217946,0.00004365152,0.000008507113,0.00008844848,0.0001126837,0.00003425114],"category_scores_gemma":[0.0001659577,0.00006539579,0.00003117062,0.0001611871,0.000131574,0.000002066748,0.0001322336,0.00006738721,0.000004598859],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000006729646,"about_ca_system_score_gemma":0.00008727952,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003110986,"about_ca_topic_score_gemma":0.00002898303,"domain_scores_codex":[0.9992061,0.00008398874,0.0001896217,0.0001987769,0.0001848535,0.0001367226],"domain_scores_gemma":[0.9991435,0.00002110497,0.00006024968,0.0001737216,0.0005616141,0.00003975781],"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":[0.0002522601,0.00004964407,0.02097576,0.00004727774,0.00004831391,8.680964e-8,0.0001692141,0.00003177059,0.9757878,0.0004456027,0.001207332,0.0009849793],"study_design_scores_gemma":[0.003169126,0.003285337,0.2497355,0.00005236228,0.0000244816,0.000002727973,0.001987452,0.001038021,0.6957889,0.0007085987,0.04386099,0.0003465239],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9979514,0.0004642453,0.0001645429,0.00006994225,0.00006445921,0.0002052473,0.00003504053,0.000001132575,0.001043973],"genre_scores_gemma":[0.9989432,0.00035991,0.0001998135,0.00002504579,0.00007614076,0.000007194237,0.00006160857,0.00001226382,0.0003148783],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2799989,"threshold_uncertainty_score":0.2666763,"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."}}