{"id":"W3190126839","doi":"10.1371/journal.pbio.3001365","title":"PhyloFisher: A phylogenomic package for resolving eukaryotic relationships","year":2021,"lang":"en","type":"article","venue":"PLoS Biology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":141,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University","funders":"Ostravská Univerzita v Ostravě; Science for Life Laboratory; Dalhousie University; Deutsche Forschungsgemeinschaft; Grantová Agentura České Republiky; Division of Environmental Biology; Ministerstvo Školství, Mládeže a Tělovýchovy; US-UK Fulbright Commission; European Research Council; National Science Foundation","keywords":"Biology; Phylogenomics; Evolutionary biology; R package; Computational biology; Phylogenetics; Genetics; Clade; Gene; Computer science; Programming language","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":[0.003257299,0.00268842,0.002710916,0.004398198,0.001688749,0.002134992,0.00441363,0.001481693,0.05127444],"category_scores_gemma":[0.005549133,0.002380762,0.003014637,0.003483385,0.0008824777,0.003923571,0.005189104,0.005885291,0.03521295],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000777811,"about_ca_system_score_gemma":0.003009541,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002112412,"about_ca_topic_score_gemma":0.002313261,"domain_scores_codex":[0.9987963,0.0002826811,0.0001211012,0.0003384295,0.0003099757,0.0001514863],"domain_scores_gemma":[0.9985492,0.0006384038,0.0002307126,0.0002690667,0.0001787119,0.0001339678],"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":[0.001624281,0.0002185533,0.008437144,0.006934356,0.001229488,0.001151385,0.002018873,0.00886683,0.05407501,0.01612294,0.7551455,0.1441756],"study_design_scores_gemma":[0.0007040687,0.0002084171,0.01119562,0.0007553731,0.0004280568,0.001585181,0.000274556,0.05241138,0.02940537,0.03497072,0.8675931,0.0004680382],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.00723208,0.001053604,0.3892958,0.0005966463,0.0003425983,0.000442709,0.1711101,0.4249263,0.005000136],"genre_scores_gemma":[0.02944365,0.001309131,0.5793056,0.000890746,0.0001264702,0.001870513,0.2354686,0.1458109,0.00577439],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.05127444,"threshold_uncertainty_score":0.1715301,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03947841470871749,"score_gpt":0.252415528739575,"score_spread":0.2129371140308575,"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."}}