{"id":"W2170587743","doi":"10.1371/journal.pone.0029903","title":"Armadillo 1.1: An Original Workflow Platform for Designing and Conducting Phylogenetic Analysis and Simulations","year":2012,"lang":"en","type":"article","venue":"PLoS ONE","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":58,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; Université du Québec à Montréal","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Armadillo; Workflow; Phylogenetic tree; Computer science; Source code; Software; Data science; Open source; Computational biology; Bioinformatics; Software engineering; Programming language; Biology; Genetics; Ecology; Database","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001330212,0.0001153556,0.0001737709,0.0000570383,0.0001836245,0.00002570269,0.00004655205,0.00006285299,0.000005468553],"category_scores_gemma":[0.0000443026,0.000114893,0.00003450223,0.00008790173,0.00005393455,0.000002853624,0.00004885599,0.00003452885,3.906929e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000004983172,"about_ca_system_score_gemma":0.00001105005,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000006722732,"about_ca_topic_score_gemma":0.00002629043,"domain_scores_codex":[0.9993449,0.00001611901,0.0001273786,0.0002143299,0.00005962292,0.0002376442],"domain_scores_gemma":[0.9995967,0.00003981248,0.00005325646,0.0001421131,0.00005842509,0.0001097054],"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":[0.00002045218,0.0001088699,0.2605318,0.00001870957,0.0008139209,6.359064e-8,0.0001814443,0.0001262259,0.7370463,0.00002867949,0.000002621128,0.00112088],"study_design_scores_gemma":[0.001318017,0.0007012415,0.1114136,0.00002624184,0.003582783,0.000005898371,0.0004765236,0.007367072,0.8730738,0.0004872213,0.0008439831,0.0007037066],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9952127,0.002589599,0.001887705,0.00002024844,0.00001923086,0.0001940051,0.00003185532,0.000003451476,0.00004117636],"genre_scores_gemma":[0.9582801,0.000176096,0.04111058,0.00005488567,0.0002485464,0.00002382366,0.00004904789,0.00001472155,0.00004220615],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1491183,"threshold_uncertainty_score":0.4685199,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1023548461067772,"score_gpt":0.2816744720881668,"score_spread":0.1793196259813896,"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."}}