{"id":"W3182507784","doi":"10.1093/bioinformatics/btab328","title":"Gene tree and species tree reconciliation with endosymbiotic gene transfer","year":2021,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":15,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; Université de Sherbrooke","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Biology; Genome; Gene duplication; Horizontal gene transfer; Mitochondrial DNA; Gene; Nuclear gene; Genetics; Genome evolution; Computational biology; Eukaryote; Evolutionary biology","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":[0.002511637,0.001382859,0.001970477,0.002930133,0.001559764,0.002033455,0.003256858,0.002539392,0.005799271],"category_scores_gemma":[0.01201018,0.0006451239,0.001842503,0.002750641,0.001451208,0.003361699,0.002350106,0.002023036,0.001245509],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.002170599,"about_ca_system_score_gemma":0.002219161,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003208549,"about_ca_topic_score_gemma":0.004460683,"domain_scores_codex":[0.9984862,0.0005211306,0.00006932,0.0004363311,0.0002514619,0.0002355474],"domain_scores_gemma":[0.9946238,0.003386629,0.000466299,0.0006624304,0.0005213911,0.0003394687],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0007069801,0.000222255,0.003367733,0.0003946811,0.0001458659,0.0002949009,0.0005078029,0.8042471,0.003507057,0.0234358,0.007229403,0.1559405],"study_design_scores_gemma":[0.00007253142,0.00009846884,0.0005975659,0.00003196193,0.00004515138,0.0001539243,0.0001206748,0.955658,0.001847125,0.03923545,0.00211945,0.00001961736],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.207006,0.001060544,0.7786772,0.00152887,0.0001489793,0.0002813623,0.001450234,0.00426666,0.005580103],"genre_scores_gemma":[0.3459969,0.0002322233,0.6472078,0.0001994974,0.0000911407,0.0002713162,0.002886996,0.0008505506,0.002263612],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.005799271,"threshold_uncertainty_score":0.01940048,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01358633206831196,"score_gpt":0.1953352262558264,"score_spread":0.1817488941875145,"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."}}