{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.008076434,0.00388718,0.004458174,0.005156721,0.00163149,0.003562658,0.004958983,0.001636139,0.1113875],"category_scores_gemma":[0.01600292,0.002824513,0.003250452,0.004716236,0.000984747,0.004927773,0.005471962,0.005781809,0.07367041],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001123698,"about_ca_system_score_gemma":0.003774617,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003678696,"about_ca_topic_score_gemma":0.003225029,"domain_scores_codex":[0.9955635,0.00160005,0.0006574291,0.0008491281,0.000985824,0.0003440302],"domain_scores_gemma":[0.9949257,0.002962044,0.0003781333,0.0006772724,0.0007998917,0.0002569923],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0006916141,0.0001617901,0.002300375,0.003791614,0.0006547627,0.0003691546,0.0008033513,0.005707303,0.008099309,0.02164425,0.7653986,0.1903779],"study_design_scores_gemma":[0.0003226816,0.000113703,0.002775589,0.0007044412,0.0002631515,0.0004213531,0.000123727,0.02552578,0.008991228,0.0386188,0.9218611,0.0002783654],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.002484104,0.001791157,0.6163235,0.000617657,0.0009455778,0.0008074064,0.1166603,0.2515541,0.008816154],"genre_scores_gemma":[0.009976787,0.001338309,0.7286301,0.001375336,0.0002021206,0.00575617,0.1620382,0.07966363,0.01101928],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.1113875,"threshold_uncertainty_score":0.3726284,"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."}}