{"id":"W4298119578","doi":"10.1101/2022.09.28.509880","title":"From comparative gene content and gene order to ancestral contigs, chromosomes and karyotypes","year":2022,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Saskatchewan; University of Ottawa","funders":"","keywords":"Phylogenetic tree; Biology; Ploidy; Contig; Ancestor; Genome; Evolutionary biology; Genetics; Gene; Phylogenetic network; Karyotype; Chromosome","routes":{"ca_aff":true,"ca_fund":false,"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":[0.000660404,0.0002642018,0.0003131895,0.001887788,0.0003384623,0.0009568417,0.000362199,0.0002302021,0.003736529],"category_scores_gemma":[0.003531395,0.0003079115,0.0002347989,0.001487544,0.0005117311,0.000551778,0.0006744424,0.0006032613,0.000956488],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003872793,"about_ca_system_score_gemma":0.0003310491,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001811166,"about_ca_topic_score_gemma":0.002819239,"domain_scores_codex":[0.9997472,0.00005308659,0.000012289,0.0001113195,0.00005558585,0.00002061757],"domain_scores_gemma":[0.9987012,0.0007282159,0.0001349119,0.0002230945,0.000164969,0.00004751021],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001316953,0.0001098113,0.2426258,0.0004993138,0.0002610277,0.0004114229,0.001122288,0.07789259,0.4214603,0.0216525,0.003619543,0.2290285],"study_design_scores_gemma":[0.00008278207,0.0001959173,0.4271429,0.0001043858,0.0001734317,0.0007599565,0.0007357855,0.325924,0.1766857,0.04575802,0.02230963,0.000127647],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"methods","genre_scores_codex":[0.8836749,0.0003298419,0.1052123,0.0001242739,0.00001065687,0.00001920629,0.004803654,0.001540623,0.004284577],"genre_scores_gemma":[0.8971327,0.0002353682,0.09327538,0.00004905456,0.00001030343,0.00003967191,0.007509848,0.0005025441,0.001245226],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.003736529,"threshold_uncertainty_score":0.01249993,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02973181827101199,"score_gpt":0.2412825550614671,"score_spread":0.2115507367904552,"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."}}