{"id":"W4377224888","doi":"10.1101/gr.277669.123","title":"A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings","year":2023,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":12,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University","funders":"Ministry of Education, India; National Science Foundation","keywords":"Phylogenetic tree; Phylogenetic network; Biology; Phylogenetics; Computational phylogenetics; Tree (set theory); Taxon; Evolutionary biology; Lineage (genetic); Phylogenetic comparative methods; Tree rearrangement; Combinatorics; Mathematics; Genetics; Ecology; Gene","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":[0.001332509,0.001317987,0.0009152234,0.002604131,0.001446426,0.001639104,0.002134258,0.001163083,0.009692169],"category_scores_gemma":[0.005387774,0.001013824,0.001398177,0.002386472,0.0007638908,0.00308978,0.001621325,0.002303597,0.003491431],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008136577,"about_ca_system_score_gemma":0.002019463,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00408474,"about_ca_topic_score_gemma":0.009263491,"domain_scores_codex":[0.9992297,0.000145354,0.00006058691,0.000246293,0.0002609368,0.00005701468],"domain_scores_gemma":[0.9983088,0.0008602745,0.0001740983,0.0002813616,0.0002650511,0.0001104426],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0005676061,0.0002225822,0.008313576,0.0007532308,0.0003474953,0.0004186696,0.0007684131,0.08291555,0.03608297,0.02752212,0.03508434,0.8070034],"study_design_scores_gemma":[0.0001285841,0.00007627025,0.001513572,0.00005972197,0.00006287626,0.0003948896,0.0001572795,0.9249198,0.01013594,0.04299656,0.01949677,0.00005767045],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.00873414,0.0001394094,0.9746807,0.0001335344,0.00004903026,0.0000841796,0.0009678673,0.01428843,0.0009227513],"genre_scores_gemma":[0.03221022,0.00009913765,0.9631625,0.00005884651,0.00002929754,0.000113385,0.002290988,0.0009084764,0.001127104],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.009692169,"threshold_uncertainty_score":0.0324235,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04699143009193168,"score_gpt":0.3459081032769009,"score_spread":0.2989166731849692,"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."}}