{"id":"W2036325355","doi":"10.1093/molbev/msm229","title":"Alternative Methods for Concatenation of Core Genes Indicate a Lack of Resolution in Deep Nodes of the Prokaryotic Phylogeny","year":2007,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":100,"is_retracted":false,"has_abstract":true,"ca_institutions":"Atlantic School of Theology; Dalhousie University; Canadian Institute for Advanced Research","funders":"Canadian Institutes of Health Research","keywords":"Concatenation (mathematics); Phylogenetic tree; Biology; Congruence (geometry); Phylogenetics; Core (optical fiber); Tree (set theory); Gene; Evolutionary biology; Phylogenetic network; Phylogenomics; Computational biology; Phylogenetic comparative methods; Genetics; Computer science; Mathematics; Combinatorics","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":[0.0005840207,0.00008383793,0.0001663678,0.00006629604,0.00003213113,6.892703e-7,0.00009780327,0.0001392312,3.275215e-7],"category_scores_gemma":[0.0001443131,0.00006565268,0.00006637962,0.00009713459,0.0002980897,7.007512e-7,0.00007830324,0.00003511968,3.520433e-8],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001187153,"about_ca_system_score_gemma":0.00003014474,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00007497617,"about_ca_topic_score_gemma":0.00007190924,"domain_scores_codex":[0.9992787,0.0001028991,0.0002813748,0.0001750338,0.00003361588,0.000128431],"domain_scores_gemma":[0.9994637,0.00003567341,0.0002174579,0.0001322214,0.0001368969,0.00001409919],"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":[0.0001540134,0.00003517849,0.06357801,0.00004096969,0.00006495595,6.683259e-8,0.00009244533,0.000352658,0.928436,0.004361031,0.000001003821,0.002883629],"study_design_scores_gemma":[0.000483923,0.0002608206,0.2469971,0.00001209609,0.00002981059,0.000002065394,0.0000632834,0.001072219,0.7421588,0.008815125,0.00004360244,0.00006123968],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8077393,0.005217444,0.1866402,0.00002279515,0.0000676911,0.0002630012,0.00001721965,5.462438e-7,0.00003184543],"genre_scores_gemma":[0.9899109,0.0001877749,0.009813543,0.00002086952,0.00001859097,0.00001546688,0.0000222514,0.000005817124,0.000004814697],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1862773,"threshold_uncertainty_score":0.2677239,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0305068380178356,"score_gpt":0.3556485436813612,"score_spread":0.3251417056635256,"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."}}