{"id":"W1893179182","doi":"10.1111/zsc.12122","title":"A case study to estimate the applicability of secondary structures of<scp>SSU</scp>‐<scp>rRNA</scp>gene in taxonomy and phylogenetic analyses of ciliates","year":2015,"lang":"en","type":"article","venue":"Zoologica Scripta","topic":"Protist diversity and phylogeny","field":"Biochemistry, Genetics and Molecular Biology","cited_by":27,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Guelph","funders":"National Natural Science Foundation of China","keywords":"Phylogenetic tree; Biology; Ribosomal RNA; Phylogenetics; Evolutionary biology; Phylogenetic network; Gene; Genetics; Protein secondary structure","routes":{"ca_aff":true,"ca_fund":false,"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":[0.0005135731,0.0002082832,0.0004350494,0.00007540399,0.00006013254,0.00001278591,0.0004061918,0.0001311107,0.000004479054],"category_scores_gemma":[0.0006806789,0.000152263,0.00008950973,0.00022649,0.0003621382,0.000005445232,0.0005248597,0.0001229452,8.750035e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001035128,"about_ca_system_score_gemma":0.00008840737,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006474445,"about_ca_topic_score_gemma":0.0003390455,"domain_scores_codex":[0.9985099,0.0002466361,0.0003989171,0.0004510931,0.0001521957,0.0002412862],"domain_scores_gemma":[0.9988254,0.000083916,0.0002263142,0.0005747764,0.0001661363,0.0001234285],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00005700348,0.0004900119,0.6523572,0.0000888843,0.0002145543,0.00008908069,0.001447921,0.0002963938,0.3429588,0.00003675428,0.0008874015,0.001076063],"study_design_scores_gemma":[0.001316407,0.002202229,0.5287443,0.000009606719,0.0001785475,0.0001562122,0.01259909,0.0000468382,0.4523752,0.001142651,0.001125473,0.0001033956],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9962485,0.002059852,0.0001365106,0.00001021391,0.00006899513,0.0009214081,0.0001828982,0.00000559845,0.0003659847],"genre_scores_gemma":[0.998107,0.00002086932,0.001658803,0.00005999755,0.00002459544,0.00005258956,0.00002043844,0.000007691019,0.00004801752],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1236128,"threshold_uncertainty_score":0.6209106,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06450497872057587,"score_gpt":0.3131627837707278,"score_spread":0.2486578050501519,"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."}}