{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00006967578,0.0001514551,0.0001540002,0.00002463985,0.00008744788,0.00004040839,0.00006937391,0.00008314673,0.00001026309],"category_scores_gemma":[0.00002286047,0.0001276389,0.00004615761,0.00006835172,0.00007051108,0.000002319314,0.00005260715,0.00004261099,0.000005268969],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000103945,"about_ca_system_score_gemma":0.00007857582,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000002342728,"about_ca_topic_score_gemma":0.0001192365,"domain_scores_codex":[0.9993128,0.00001484736,0.0002250509,0.0001598299,0.0001013402,0.0001861209],"domain_scores_gemma":[0.9995461,0.00001093824,0.00003853011,0.0002375931,0.0001027027,0.00006413704],"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":[0.00006702745,0.00004647581,0.0081312,0.00008109961,0.0002306595,0.000007517791,0.0007033645,0.00006199735,0.9721432,0.0001690848,0.000468419,0.01788996],"study_design_scores_gemma":[0.001140774,0.0003510412,0.0385722,0.00001180086,0.00007147487,0.0001152985,0.0006219111,0.0004199117,0.9409761,0.00003637682,0.0173777,0.0003054612],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9901589,0.001455017,0.003160262,0.0001761225,0.00009545087,0.0001280542,0.00004676367,0.000005270675,0.004774209],"genre_scores_gemma":[0.9793462,0.002183122,0.01682529,0.0002639672,0.0001374735,0.000008554769,0.000142343,0.00001597354,0.00107704],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03116714,"threshold_uncertainty_score":0.5204962,"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."}}