{"id":"W3127571043","doi":"10.1093/molbev/msab037","title":"Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding","year":2021,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"Molecular Biology Techniques and Applications","field":"Biochemistry, Genetics and Molecular Biology","cited_by":16,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ontario Brain Institute; Alberta Children's Hospital; University of Calgary","funders":"Natural Sciences and Engineering Research Council of Canada; Alberta Children's Hospital Research Institute","keywords":"Biology; Linkage (software); Scaffold; Evolutionary biology; Haplotype; Computational biology; Genetics; Genetic linkage; Gene; Genotype; Engineering","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":[],"consensus_categories":[],"category_scores_codex":[0.001821681,0.0006000401,0.0006868735,0.001921552,0.0005310845,0.0009770688,0.00100111,0.0005705606,0.0008957637],"category_scores_gemma":[0.005310548,0.0006975656,0.0008447788,0.001431406,0.0005753762,0.001341336,0.001435108,0.0006695504,0.000305953],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004676966,"about_ca_system_score_gemma":0.001094532,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002354617,"about_ca_topic_score_gemma":0.003915168,"domain_scores_codex":[0.9994071,0.0002180429,0.00003566388,0.000180654,0.0001166201,0.00004202576],"domain_scores_gemma":[0.9978554,0.001249326,0.0002355046,0.0004020298,0.000172334,0.00008535677],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0002708243,0.0001729033,0.02815217,0.0002441943,0.0003373063,0.0002737271,0.0003056376,0.7976366,0.03222018,0.01456104,0.0007602341,0.1250652],"study_design_scores_gemma":[0.00001097429,0.00003890746,0.001367314,0.000005218774,0.00002180709,0.00003724591,0.0000274899,0.9876045,0.003721012,0.006688739,0.0004641615,0.0000127243],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.2139548,0.0001481977,0.7834537,0.00006398528,0.00001682634,0.00004031474,0.0004666176,0.001311137,0.000544453],"genre_scores_gemma":[0.5792513,0.0001467926,0.4186351,0.00003767269,0.00002021435,0.0001056678,0.001294976,0.0002233049,0.0002848712],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.002354617,"threshold_uncertainty_score":0.009634078,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.003922913395235469,"score_gpt":0.2634000003306528,"score_spread":0.2594770869354173,"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."}}