{"id":"W2256500242","doi":"10.1093/bioinformatics/btv763","title":"Sampletrees and Rsampletrees: sampling gene genealogies conditional on SNP genotype data","year":2016,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genetic Associations and Epidemiology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University; University of Ottawa","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; Michael Smith Health Research BC","keywords":"R package; Computer science; Documentation; Markov chain Monte Carlo; Source code; Code (set theory); SNP; Genotype; Markov chain; Data mining; Monte Carlo method; Programming language; Statistics; Biology; Genetics; Gene; Single-nucleotide polymorphism; Mathematics","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":[0.0003295148,0.0001586773,0.0001696465,0.00005333906,0.0001395213,0.00002419404,0.000306487,0.0001564793,0.00003493796],"category_scores_gemma":[0.0007680391,0.0001105233,0.00003572114,0.00004806014,0.0001310685,0.00001136611,0.0003412287,0.00004632945,0.00005358516],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001790268,"about_ca_system_score_gemma":0.00006524144,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001287955,"about_ca_topic_score_gemma":0.00003527189,"domain_scores_codex":[0.9989595,0.0000365276,0.000344484,0.0002533288,0.0001231565,0.0002829352],"domain_scores_gemma":[0.9988902,0.0001622005,0.0001575747,0.0006372445,0.00006943199,0.00008337852],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0003453915,0.000339663,0.2388954,0.0002040971,0.001235218,0.000005479118,0.0005232203,0.0009510468,0.2014864,0.01062754,0.1837512,0.3616354],"study_design_scores_gemma":[0.002734463,0.001211119,0.4859733,0.0000655457,0.000108222,0.00009009698,0.0004829655,0.003946206,0.007918033,0.005672575,0.4905693,0.001228193],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.680143,0.000682293,0.3131604,0.001457708,0.0002825398,0.0002787414,0.002836462,0.00004927048,0.001109574],"genre_scores_gemma":[0.8526464,0.001690854,0.1399333,0.001606405,0.0004387741,0.00001600257,0.003378181,0.00002552419,0.0002645351],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3604072,"threshold_uncertainty_score":0.4507008,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.09098278476994492,"score_gpt":0.3176090273950153,"score_spread":0.2266262426250704,"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."}}