{"id":"W2140771555","doi":"10.1093/molbev/msu231","title":"Alignment Errors Strongly Impact Likelihood-Based Tests for Comparing Topologies","year":2014,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":26,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University","funders":"Natural Sciences and Engineering Research Council of Canada; Tel Aviv University; Israel Science Foundation","keywords":"Network topology; Tree (set theory); Parametric statistics; Statistical hypothesis testing; Sequence (biology); Phylogenetic tree; Phylogenomics; Computer science; Test case; Test (biology); Set (abstract data type); Machine learning; Data mining; Biology; Algorithm; Statistics; Mathematics; Paleontology","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":["metaresearch"],"consensus_categories":[],"category_scores_codex":[0.06126041,0.001796579,0.002165835,0.003856047,0.001882869,0.004458676,0.003261535,0.003443882,0.002223337],"category_scores_gemma":[0.2990616,0.0009319916,0.001426254,0.005322228,0.005732032,0.006418586,0.004476767,0.00614896,0.0008731892],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0012193,"about_ca_system_score_gemma":0.001359948,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005987958,"about_ca_topic_score_gemma":0.0007450197,"domain_scores_codex":[0.9275388,0.05394482,0.002886994,0.005167402,0.009483794,0.0009781829],"domain_scores_gemma":[0.4963981,0.4718097,0.01389193,0.01219907,0.004609607,0.00109164],"domain_codex":null,"domain_gemma":"methods","domain_candidate":"methods","domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001763311,0.0004339101,0.122161,0.002075039,0.002265787,0.002226401,0.002046913,0.3074701,0.0322678,0.1634206,0.00590991,0.3579592],"study_design_scores_gemma":[0.0002536058,0.000778909,0.02819865,0.0003447887,0.0003445192,0.001730015,0.0005242365,0.6133991,0.03743352,0.3076651,0.008928942,0.0003985438],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.1276673,0.00271053,0.8625082,0.00167618,0.0002681653,0.0001660395,0.0005579746,0.001186187,0.003259375],"genre_scores_gemma":[0.7001474,0.000963374,0.2950664,0.0006565872,0.0002717006,0.0004163439,0.001040932,0.0008480291,0.0005891763],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.9387396,"threshold_uncertainty_score":0.3239799,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01244713305034438,"score_gpt":0.2882270291329186,"score_spread":0.2757798960825742,"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."}}