{"id":"W1981693566","doi":"10.3390/computation2040182","title":"Incongruencies in Vaccinia Virus Phylogenetic Trees","year":2014,"lang":"en","type":"article","venue":"Computation","topic":"Poxvirus research and outbreaks","field":"Immunology and Microbiology","cited_by":14,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Lethbridge; University of Victoria","funders":"University of Victoria","keywords":"Cowpox virus; Cowpox; Biology; Phylogenetic tree; Genome; Orthopoxvirus; Clade; Vaccinia; Modified vaccinia Ankara; Poxviridae; Virology; Ectromelia virus; Genetics; Evolutionary biology; Gene","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":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0001762134,0.00007004763,0.0001112639,0.0001242652,0.00005567728,0.00001192747,0.0001016153,0.00008092303,0.00009464243],"category_scores_gemma":[0.00009842793,0.00006416153,0.00002336958,0.000112281,0.00004999989,0.00004287777,0.0000378504,0.0001155645,0.0007908559],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002374206,"about_ca_system_score_gemma":0.00002617448,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002661254,"about_ca_topic_score_gemma":0.0006737827,"domain_scores_codex":[0.9993128,0.0001798935,0.0001370281,0.0001411901,0.00002336714,0.0002057442],"domain_scores_gemma":[0.9996985,0.000140207,0.00003217394,0.00008413517,0.00003028027,0.00001471923],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0001104365,0.00008282343,0.0185545,0.00001080824,0.00002404595,0.000002899651,0.000533732,0.0009642905,0.7257202,0.0005984806,0.001600477,0.2517973],"study_design_scores_gemma":[0.00214937,0.0003473362,0.866879,0.00003149092,0.000007489426,0.00001581018,0.00007062181,0.002981816,0.1077679,0.004229986,0.01530057,0.0002185505],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9950042,0.0007939796,0.001726861,0.0001051971,0.0001749084,0.00009324949,0.00000393595,0.0000365125,0.002061159],"genre_scores_gemma":[0.9994718,0.00002686025,0.00008809517,0.0001008606,0.00002168713,0.0000090133,0.00004968612,0.000005669759,0.0002263669],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8483246,"threshold_uncertainty_score":0.9999871,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01499583527062454,"score_gpt":0.2683748898216397,"score_spread":0.2533790545510152,"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."}}