{"id":"W2125867054","doi":"10.1093/molbev/mst064","title":"DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution","year":2013,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1203,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ontario Genomics; University of Ottawa","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Biology; Phylogenetic tree; Phylogenetics; Maximum parsimony; GenBank; Multiple sequence alignment; Software; Computational biology; Molecular evolution; Sequence alignment; Computer science; Genetics; Gene; Clade; Peptide sequence","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":[0.0001848982,0.0002425859,0.0003432127,0.0001809628,0.000127724,0.00001862609,0.0002155881,0.0003486245,0.000003951022],"category_scores_gemma":[0.0001477547,0.000234998,0.00008622336,0.0002091412,0.000287683,0.000004213289,0.000447565,0.00009246607,0.000002773716],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002427723,"about_ca_system_score_gemma":0.00004030899,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0004777526,"about_ca_topic_score_gemma":0.0001971723,"domain_scores_codex":[0.9983141,0.0001675523,0.000279915,0.0008168142,0.00004013914,0.0003814925],"domain_scores_gemma":[0.9990661,0.00003811258,0.0001032704,0.0005793006,0.0001322051,0.00008104192],"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":[0.00004556125,0.00003264558,0.1771868,0.00002000571,0.0004132616,0.000001288483,0.00002052588,0.0000530482,0.8183264,0.002781956,0.0001054245,0.001013152],"study_design_scores_gemma":[0.002966287,0.001287172,0.8962635,0.00002202802,0.0008209369,0.00003757139,0.0002900458,0.005579141,0.02680639,0.0612909,0.003525788,0.001110176],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6611701,0.009885965,0.3281754,0.000170345,0.00006046847,0.0003687837,0.000145022,0.000005458509,0.00001847594],"genre_scores_gemma":[0.9868071,0.0003554501,0.01114171,0.0002347158,0.0000483747,0.0001079833,0.001268717,0.00001759054,0.00001835576],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.79152,"threshold_uncertainty_score":0.9582941,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01289526375414443,"score_gpt":0.2775978353772914,"score_spread":0.264702571623147,"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."}}