{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.003458076,0.001087454,0.001149803,0.001958565,0.001044171,0.001305459,0.001173595,0.001148187,0.001394371],"category_scores_gemma":[0.009400176,0.0005864777,0.001523453,0.001320112,0.001100935,0.001315441,0.001697994,0.002334834,0.0008796746],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007561276,"about_ca_system_score_gemma":0.001337416,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007486313,"about_ca_topic_score_gemma":0.001253859,"domain_scores_codex":[0.9981622,0.0005689634,0.0001629564,0.0005989624,0.0004162933,0.00009062187],"domain_scores_gemma":[0.9967693,0.00134306,0.0004745566,0.000631362,0.0005796661,0.0002021136],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0007797794,0.0002109083,0.01997301,0.0004987003,0.0005300555,0.0005966017,0.001079318,0.0712973,0.2208177,0.02228621,0.002150819,0.6597797],"study_design_scores_gemma":[0.0001253968,0.0003510962,0.009992233,0.00009926572,0.0002007251,0.001189363,0.0001221739,0.8779725,0.07171375,0.0250857,0.01300511,0.000142725],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.03412711,0.0003004821,0.9635106,0.00009214315,0.00008385122,0.00004824373,0.00007573203,0.001329193,0.000432547],"genre_scores_gemma":[0.1043968,0.0001496171,0.8935856,0.00008116812,0.00005030547,0.0001017236,0.0002891368,0.0004315743,0.0009141195],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.003458076,"threshold_uncertainty_score":0.01828831,"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."}}