{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00009647784,0.00007995591,0.0001436108,0.00003796813,0.00002521942,0.000002541889,0.00003400677,0.0001832502,0.000002192938],"category_scores_gemma":[0.00006371787,0.00008028604,0.00002831362,0.00007259857,0.0002470422,0.000002715817,0.00005375415,0.00006321901,1.565076e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000006721692,"about_ca_system_score_gemma":0.00002707721,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003905999,"about_ca_topic_score_gemma":0.00002224617,"domain_scores_codex":[0.9993677,0.0001041896,0.0001710708,0.0002418123,0.00002168313,0.00009353406],"domain_scores_gemma":[0.9997282,0.00001157029,0.00006933254,0.0001109751,0.00005689921,0.00002302908],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00002719713,0.00004874521,0.005960071,0.00001376949,0.00001464155,6.453105e-7,0.000013862,0.00000183913,0.9761067,0.01298495,0.00003289482,0.004794701],"study_design_scores_gemma":[0.000264564,0.0001870338,0.006540301,0.00002161777,0.00001691201,0.00003607241,0.00003773859,0.0002475329,0.9873433,0.005105979,0.0001145855,0.0000844289],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8093169,0.001003063,0.1894356,0.00005907813,0.00001681261,0.00007044966,0.00003710767,0.000003612542,0.00005742655],"genre_scores_gemma":[0.9926809,0.0002320591,0.006738989,0.00002667512,0.00001489239,0.00001063221,0.0002813938,0.000005547472,0.000008897149],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.183364,"threshold_uncertainty_score":0.327397,"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."}}