{"id":"W2118670112","doi":"10.1093/molbev/msi238","title":"Statistical Alignment of Retropseudogenes and Their Functional Paralogs","year":2005,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":8,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal","funders":"","keywords":"Biology; Pseudogene; Genetics; Gene; Homology (biology); Stop codon; Computational biology; Most recent common ancestor; Sequence (biology); Molecular evolution; Coding region; Phylogenetic tree; Evolutionary biology; Genome","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":[0.001771795,0.0003426892,0.000476936,0.001433657,0.0005734816,0.0009508033,0.0009299309,0.0006293278,0.00203709],"category_scores_gemma":[0.008045996,0.0004475125,0.0006243819,0.001379168,0.0007860587,0.001278933,0.0006053524,0.0009603131,0.0007949167],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006192954,"about_ca_system_score_gemma":0.0007209078,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007404527,"about_ca_topic_score_gemma":0.001132045,"domain_scores_codex":[0.9989846,0.0004260994,0.00005579723,0.0002613656,0.00021394,0.00005817214],"domain_scores_gemma":[0.9970818,0.002019049,0.0003751396,0.000246765,0.0001764785,0.0001006834],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"observational","study_design_scores_codex":[0.0008512906,0.0002070777,0.03294958,0.0003949724,0.0002737909,0.001189768,0.000431589,0.5617062,0.04889834,0.1909911,0.004175527,0.1579308],"study_design_scores_gemma":[0.00003861822,0.00009552426,0.004704549,0.00001802845,0.00003151759,0.0004396396,0.00006834159,0.862901,0.006639167,0.1198058,0.005228396,0.00002940667],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.2126768,0.0006231244,0.7816928,0.0004654726,0.00004982255,0.00005703158,0.001079054,0.001117154,0.002238689],"genre_scores_gemma":[0.7584761,0.0005385011,0.2344586,0.0001381732,0.00006863352,0.0001952956,0.003876049,0.0005573305,0.001691311],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.00203709,"threshold_uncertainty_score":0.009370267,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007119364549538367,"score_gpt":0.2286564585350696,"score_spread":0.2215370939855313,"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."}}