{"id":"W2604358300","doi":"10.1093/jhered/esx033","title":"DAMBE6: New Tools for Microbial Genomics, Phylogenetics, and Molecular Evolution","year":2017,"lang":"en","type":"article","venue":"Journal of Heredity","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":411,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa","funders":"","keywords":"Biology; Phylogenetic tree; Computational biology; Multiple sequence alignment; Alignment-free sequence analysis; Phylogenetics; Pairwise comparison; Genetics; Genomics; Sequence alignment; Evolutionary biology; Gene; Genome; Computer science; Peptide sequence; Artificial intelligence","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002334269,0.0001220739,0.0001953418,0.00002256894,0.0001961521,0.000104426,0.0002639438,0.0001073082,0.000002583168],"category_scores_gemma":[0.0002126725,0.000114584,0.0001344976,0.000007479965,0.0001025463,0.000003344526,0.000144227,0.00006860845,6.05025e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002165248,"about_ca_system_score_gemma":0.000164531,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002388121,"about_ca_topic_score_gemma":0.00004647033,"domain_scores_codex":[0.9993188,0.00001877779,0.0002582825,0.000163657,0.00007148082,0.0001689714],"domain_scores_gemma":[0.9990193,0.00001372794,0.0003877946,0.0002854507,0.0001864172,0.0001073093],"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":[0.0001361571,0.00002372398,0.003181058,0.00001158757,0.0001268055,0.000003108512,0.00003323442,0.00003400991,0.9844974,0.00006859056,0.005749066,0.006135239],"study_design_scores_gemma":[0.004211252,0.001632071,0.1275975,0.0000396881,0.0002332228,0.0002220966,0.0001529406,0.00005637659,0.658893,0.005945708,0.2005122,0.0005038109],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.985605,0.004774312,0.008141433,0.0004204905,0.0007703179,0.0001390433,0.00004545039,6.436502e-7,0.0001033194],"genre_scores_gemma":[0.9895909,0.0007261862,0.007802732,0.00009000553,0.001673301,0.000001427484,0.00000475073,0.00001556584,0.00009512984],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3256043,"threshold_uncertainty_score":0.4672599,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02084997283991802,"score_gpt":0.2623546987464235,"score_spread":0.2415047259065055,"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."}}