{"id":"W3081731525","doi":"10.3390/life10090171","title":"Improving Phylogenetic Signals of Mitochondrial Genes Using a New Method of Codon Degeneration","year":2020,"lang":"en","type":"article","venue":"Life","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Nonsynonymous substitution; Codon usage bias; Synonymous substitution; Phylogenetic tree; Biology; Genetics; Genetic code; Phylogenetics; Gene; Mitochondrial DNA; Stop codon; Genome","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":[0.00006639941,0.0001197178,0.0002283628,0.00002127216,0.00003209019,0.000006456802,0.000123201,0.00008752726,0.000009475938],"category_scores_gemma":[0.0001231174,0.0001188995,0.00009952562,0.00007743962,0.00003299776,6.026759e-7,0.00010506,0.00002899052,6.10447e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000003082824,"about_ca_system_score_gemma":0.000162927,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001150279,"about_ca_topic_score_gemma":0.00001175502,"domain_scores_codex":[0.9991613,0.00006274867,0.0003081527,0.00024177,0.0000974038,0.0001286016],"domain_scores_gemma":[0.9994394,0.00001547033,0.0001989169,0.0001581688,0.00008797968,0.0001000551],"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":[0.00008088557,0.00001342667,0.001177823,0.00004053039,0.00007299911,1.999242e-7,0.0001311578,0.006035259,0.9884975,0.00002360969,0.000152405,0.003774217],"study_design_scores_gemma":[0.0004717676,0.0003001189,0.0003034285,0.000005315547,0.00006050775,0.000001512217,0.00005766679,0.003603354,0.9938791,0.00002843485,0.001170076,0.0001186913],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8585659,0.00409886,0.1368882,0.00009374827,0.0001317406,0.0001555444,0.00002482265,0.000001742691,0.00003946204],"genre_scores_gemma":[0.8836618,0.0001182105,0.1151392,0.0002309045,0.0007959645,0.000003134957,0.00001162273,0.0000174513,0.0000216882],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02509593,"threshold_uncertainty_score":0.4848582,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03652397737041888,"score_gpt":0.2844030946615052,"score_spread":0.2478791172910863,"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."}}