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] } ], "combinatorial_sweep_32_chains": [ { "regime_id": "Regime 1: 100% Native Rust (super-blast -> gotoh-msa -> popgen-blind-dualpass -> RY3 -> felsenstein-modeltest -> runie-mcmc-skyline)", "chain_rank_in_regime": 1, "global_rank": 1, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest (GTR+F+R4) -> runie-mcmc-skyline (10k gen, 20% burn-in) -> dnds-selection", "model_name": "GTR+F+R4", "k_free_params": 137, "marginal_ln_l": -342000.8558, "delta_ln_l_vs_best": 0, "aic": 684275.7116, "bic": 685398.073, "rcfv": 0.007, "bootstrap_support_pct": 99.6, "posterior_prob": 0.9999, "msa_time_ms": 9680, "modeltest_time_ms": 98, "tree_mcmc_time_ms": 2980, "total_cpu_time_ms": 12758 }, { "regime_id": "Regime 1: 100% Native Rust (super-blast -> gotoh-msa -> popgen-blind-dualpass -> RY3 -> felsenstein-modeltest -> runie-mcmc-skyline)", "chain_rank_in_regime": 6, "global_rank": 2, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> 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2980, "total_cpu_time_ms": 12758 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (super-blast -> *MAFFT v7.526 -> popgen-blind-dualpass [RY3] -> *IQ-TREE v2.4.0 -> *LSD2 -> runie-mcmc-skyline -> *PAML v4.10.10)", "chain_rank_in_regime": 2, "global_rank": 8, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (GTR+F+I+G4) -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "GTR+F+I+G4", "k_free_params": 137, "marginal_ln_l": -382501.7434, "delta_ln_l_vs_best": -40500.8876, "aic": 765273.4868, "bic": 766379.4633, "rcfv": 0.007, "bootstrap_support_pct": 100, "posterior_prob": 1, "msa_time_ms": 119510, "modeltest_time_ms": 472750, "tree_mcmc_time_ms": 2980, "total_cpu_time_ms": 595240 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (super-blast -> *MAFFT v7.526 -> popgen-blind-dualpass [RY3] -> *IQ-TREE v2.4.0 -> *LSD2 -> runie-mcmc-skyline -> *PAML v4.10.10)", "chain_rank_in_regime": 1, "global_rank": 9, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (GTR+F+R4) -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "GTR+F+R4", "k_free_params": 139, "marginal_ln_l": -382587.681, "delta_ln_l_vs_best": -40586.8252, "aic": 765453.3621, "bic": 766592.1083, "rcfv": 0.007, "bootstrap_support_pct": 100, "posterior_prob": 1, "msa_time_ms": 119510, "modeltest_time_ms": 108594, "tree_mcmc_time_ms": 2980, "total_cpu_time_ms": 231084 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (super-blast -> *MAFFT v7.526 -> popgen-blind-dualpass [RY3] -> *IQ-TREE v2.4.0 -> *LSD2 -> runie-mcmc-skyline -> *PAML v4.10.10)", "chain_rank_in_regime": 4, "global_rank": 10, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (TIM2+F+I+G4) -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "TIM2+F+I+G4", "k_free_params": 133, "marginal_ln_l": -382643.5153, "delta_ln_l_vs_best": -40642.6595, "aic": 765553.0307, "bic": 766642.6224, "rcfv": 0.007, "bootstrap_support_pct": 100, "posterior_prob": 1, "msa_time_ms": 119510, "modeltest_time_ms": 18063, "tree_mcmc_time_ms": 2980, "total_cpu_time_ms": 140553 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (super-blast -> *MAFFT v7.526 -> popgen-blind-dualpass [RY3] -> *IQ-TREE v2.4.0 -> *LSD2 -> runie-mcmc-skyline -> *PAML v4.10.10)", "chain_rank_in_regime": 5, "global_rank": 11, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (TN+F+I+G4) -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "TN+F+I+G4", "k_free_params": 131, "marginal_ln_l": -383957.9722, "delta_ln_l_vs_best": -41957.1164, "aic": 768179.9445, "bic": 769261.3438, "rcfv": 0.007, "bootstrap_support_pct": 100, "posterior_prob": 1, "msa_time_ms": 119510, "modeltest_time_ms": 15406, "tree_mcmc_time_ms": 2980, "total_cpu_time_ms": 137896 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (super-blast -> *MAFFT v7.526 -> popgen-blind-dualpass [RY3] -> *IQ-TREE v2.4.0 -> *LSD2 -> runie-mcmc-skyline -> *PAML v4.10.10)", "chain_rank_in_regime": 3, "global_rank": 12, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (GTR+F+G4) -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "GTR+F+G4", "k_free_params": 135, "marginal_ln_l": -385394.9709, "delta_ln_l_vs_best": -43394.1151, "aic": 771057.9418, "bic": 772155.726, "rcfv": 0.007, "bootstrap_support_pct": 100, "posterior_prob": 1, "msa_time_ms": 119510, "modeltest_time_ms": 18719, "tree_mcmc_time_ms": 2980, "total_cpu_time_ms": 141209 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (super-blast -> *MAFFT v7.526 -> popgen-blind-dualpass [RY3] -> *IQ-TREE v2.4.0 -> *LSD2 -> runie-mcmc-skyline -> *PAML v4.10.10)", "chain_rank_in_regime": 6, "global_rank": 13, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (HKY+F+I+G4) -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "HKY+F+I+G4", "k_free_params": 129, "marginal_ln_l": -386110.2027, "delta_ln_l_vs_best": -44109.3469, "aic": 772482.4054, "bic": 773555.6123, "rcfv": 0.007, "bootstrap_support_pct": 100, "posterior_prob": 1, "msa_time_ms": 119510, "modeltest_time_ms": 13547, "tree_mcmc_time_ms": 2980, "total_cpu_time_ms": 136037 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (super-blast -> *MAFFT v7.526 -> popgen-blind-dualpass [RY3] -> *IQ-TREE v2.4.0 -> *LSD2 -> runie-mcmc-skyline -> *PAML v4.10.10)", "chain_rank_in_regime": 7, "global_rank": 14, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (K80+G4) -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "K80+G4", "k_free_params": 127, "marginal_ln_l": -400636.9029, "delta_ln_l_vs_best": -58636.0471, "aic": 801527.8059, "bic": 802568.2431, "rcfv": 0.007, "bootstrap_support_pct": 100, "posterior_prob": 1, "msa_time_ms": 119510, "modeltest_time_ms": 7797, "tree_mcmc_time_ms": 2980, "total_cpu_time_ms": 130287 }, { "regime_id": "Regime 1: 100% Native Rust (super-blast -> gotoh-msa -> popgen-blind-dualpass -> RY3 -> felsenstein-modeltest -> runie-mcmc-skyline)", "chain_rank_in_regime": 8, "global_rank": 15, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest (JC) -> runie-mcmc-skyline (10k gen, 20% burn-in) -> dnds-selection", "model_name": "JC", "k_free_params": 125, "marginal_ln_l": -446220.1451, "delta_ln_l_vs_best": -104219.2893, "aic": 892690.2901, "bic": 893714.3425, "rcfv": 0.007, "bootstrap_support_pct": 96.8, "posterior_prob": 0.952, "msa_time_ms": 9680, "modeltest_time_ms": 98, "tree_mcmc_time_ms": 2980, "total_cpu_time_ms": 12758 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT v7.526 -> *IQ-TREE v2.4.0 -> *LSD2 v2.4.4 -> *BEAST v1.10.4 -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10)", "chain_rank_in_regime": 2, "global_rank": 16, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (GTR+F+I+G4) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10", "model_name": "GTR+F+I+G4", "k_free_params": 137, "marginal_ln_l": -457340.8835, "delta_ln_l_vs_best": -115340.0277, "aic": 914951.767, "bic": 916057.7436, "rcfv": 0.0371, "bootstrap_support_pct": 98.2, "posterior_prob": 0.9991, "msa_time_ms": 119510, "modeltest_time_ms": 418047, "tree_mcmc_time_ms": 4320, "total_cpu_time_ms": 541877 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT v7.526 -> *IQ-TREE v2.4.0 -> *LSD2 v2.4.4 -> *BEAST v1.10.4 -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10)", "chain_rank_in_regime": 1, "global_rank": 17, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (GTR+F+R4) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10", "model_name": "GTR+F+R4", "k_free_params": 139, "marginal_ln_l": -457377.8294, "delta_ln_l_vs_best": -115376.9736, "aic": 915033.6588, "bic": 916172.4051, "rcfv": 0.0371, "bootstrap_support_pct": 98.2, "posterior_prob": 0.9991, "msa_time_ms": 119510, "modeltest_time_ms": 36813, "tree_mcmc_time_ms": 4320, "total_cpu_time_ms": 160643 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT v7.526 -> *IQ-TREE v2.4.0 -> *LSD2 v2.4.4 -> *BEAST v1.10.4 -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10)", "chain_rank_in_regime": 4, "global_rank": 18, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (TIM2+F+I+G4) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10", "model_name": "TIM2+F+I+G4", "k_free_params": 133, "marginal_ln_l": -457482.738, "delta_ln_l_vs_best": -115481.8822, "aic": 915231.476, "bic": 916321.0677, "rcfv": 0.0371, "bootstrap_support_pct": 98.2, "posterior_prob": 0.9991, "msa_time_ms": 119510, "modeltest_time_ms": 17219, "tree_mcmc_time_ms": 4320, "total_cpu_time_ms": 141049 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT v7.526 -> *IQ-TREE v2.4.0 -> *LSD2 v2.4.4 -> *BEAST v1.10.4 -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10)", "chain_rank_in_regime": 5, "global_rank": 19, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (TN+F+I+G4) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10", "model_name": "TN+F+I+G4", "k_free_params": 131, "marginal_ln_l": -459475.7491, "delta_ln_l_vs_best": -117474.8933, "aic": 919215.4983, "bic": 920296.8975, "rcfv": 0.0371, "bootstrap_support_pct": 98.2, "posterior_prob": 0.9991, "msa_time_ms": 119510, "modeltest_time_ms": 14313, "tree_mcmc_time_ms": 4320, "total_cpu_time_ms": 138143 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT v7.526 -> *IQ-TREE v2.4.0 -> *LSD2 v2.4.4 -> *BEAST v1.10.4 -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10)", "chain_rank_in_regime": 3, "global_rank": 20, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (GTR+F+G4) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10", "model_name": "GTR+F+G4", "k_free_params": 135, "marginal_ln_l": -460784.7722, "delta_ln_l_vs_best": -118783.9164, "aic": 921837.5444, "bic": 922935.3285, "rcfv": 0.0371, "bootstrap_support_pct": 98.2, "posterior_prob": 0.9991, "msa_time_ms": 119510, "modeltest_time_ms": 15484, "tree_mcmc_time_ms": 4320, "total_cpu_time_ms": 139314 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT v7.526 -> *IQ-TREE v2.4.0 -> *LSD2 v2.4.4 -> *BEAST v1.10.4 -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10)", "chain_rank_in_regime": 6, "global_rank": 21, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (HKY+F+I+G4) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10", "model_name": "HKY+F+I+G4", "k_free_params": 129, "marginal_ln_l": -462334.1424, "delta_ln_l_vs_best": -120333.2866, "aic": 924930.2849, "bic": 926003.4918, "rcfv": 0.0371, "bootstrap_support_pct": 98.2, "posterior_prob": 0.9991, "msa_time_ms": 119510, "modeltest_time_ms": 13406, "tree_mcmc_time_ms": 4320, "total_cpu_time_ms": 137236 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unrecoded Saturation + Unfiltered NUMT Pseudogene Chimera)", "chain_rank_in_regime": 2, "global_rank": 22, "tool_chain_summary": "Raw Uncleaned Supermatrix -> No RY3 / No NUMT Chimera Filter -> *IQ-TREE v2.4.0 (GTR+F+I+G4) -> Uncleaned Skyline (0-Beaker Rejected)", "model_name": "GTR+F+I+G4", "k_free_params": 137, "marginal_ln_l": -464948.4969, "delta_ln_l_vs_best": -122947.6411, "aic": 930166.9938, "bic": 931272.9704, "rcfv": 0.0407, "bootstrap_support_pct": 59.4, "posterior_prob": 0.0001, "msa_time_ms": 119510, "modeltest_time_ms": 399750, "tree_mcmc_time_ms": 4320, "total_cpu_time_ms": 523580 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unrecoded Saturation + Unfiltered NUMT Pseudogene Chimera)", "chain_rank_in_regime": 4, "global_rank": 23, "tool_chain_summary": "Raw Uncleaned Supermatrix -> No RY3 / No NUMT Chimera Filter -> *IQ-TREE v2.4.0 (TIM2+F+I+G4) -> Uncleaned Skyline (0-Beaker Rejected)", "model_name": "TIM2+F+I+G4", "k_free_params": 133, "marginal_ln_l": -465739.5574, "delta_ln_l_vs_best": -123738.7016, "aic": 931745.1149, "bic": 932834.7066, "rcfv": 0.0407, "bootstrap_support_pct": 59.4, "posterior_prob": 0.0001, "msa_time_ms": 119510, "modeltest_time_ms": 16125, "tree_mcmc_time_ms": 4320, "total_cpu_time_ms": 139955 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unrecoded Saturation + Unfiltered NUMT Pseudogene Chimera)", "chain_rank_in_regime": 1, "global_rank": 24, "tool_chain_summary": "Raw Uncleaned Supermatrix -> No RY3 / No NUMT Chimera Filter -> *IQ-TREE v2.4.0 (GTR+F+R4) -> Uncleaned Skyline (0-Beaker Rejected)", "model_name": "GTR+F+R4", "k_free_params": 139, "marginal_ln_l": -465877.3305, "delta_ln_l_vs_best": -123876.4747, "aic": 932032.661, "bic": 933171.4073, "rcfv": 0.0407, "bootstrap_support_pct": 59.4, "posterior_prob": 0.0001, "msa_time_ms": 119510, "modeltest_time_ms": 203984, "tree_mcmc_time_ms": 4320, "total_cpu_time_ms": 327814 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unrecoded Saturation + Unfiltered NUMT Pseudogene Chimera)", "chain_rank_in_regime": 5, "global_rank": 25, "tool_chain_summary": "Raw Uncleaned Supermatrix -> No RY3 / No NUMT Chimera Filter -> *IQ-TREE v2.4.0 (TN+F+I+G4) -> Uncleaned Skyline (0-Beaker Rejected)", "model_name": "TN+F+I+G4", "k_free_params": 131, "marginal_ln_l": -467975.6417, "delta_ln_l_vs_best": -125974.7859, "aic": 936215.2835, "bic": 937296.6828, "rcfv": 0.0407, "bootstrap_support_pct": 59.4, "posterior_prob": 0.0001, "msa_time_ms": 119510, "modeltest_time_ms": 13625, "tree_mcmc_time_ms": 4320, "total_cpu_time_ms": 137455 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unrecoded Saturation + Unfiltered NUMT Pseudogene Chimera)", "chain_rank_in_regime": 3, "global_rank": 26, "tool_chain_summary": "Raw Uncleaned Supermatrix -> No RY3 / No NUMT Chimera Filter -> *IQ-TREE v2.4.0 (GTR+F+G4) -> Uncleaned Skyline (0-Beaker Rejected)", "model_name": "GTR+F+G4", "k_free_params": 135, "marginal_ln_l": -468625.4569, "delta_ln_l_vs_best": -126624.6011, "aic": 937518.9138, "bic": 938616.6979, "rcfv": 0.0407, "bootstrap_support_pct": 59.4, "posterior_prob": 0.0001, "msa_time_ms": 119510, "modeltest_time_ms": 18703, "tree_mcmc_time_ms": 4320, "total_cpu_time_ms": 142533 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unrecoded Saturation + Unfiltered NUMT Pseudogene Chimera)", "chain_rank_in_regime": 6, "global_rank": 27, "tool_chain_summary": "Raw Uncleaned Supermatrix -> No RY3 / No NUMT Chimera Filter -> *IQ-TREE v2.4.0 (HKY+F+I+G4) -> Uncleaned Skyline (0-Beaker Rejected)", "model_name": "HKY+F+I+G4", "k_free_params": 129, "marginal_ln_l": -470054.4262, "delta_ln_l_vs_best": -128053.5704, "aic": 940370.8525, "bic": 941444.0593, "rcfv": 0.0407, "bootstrap_support_pct": 59.4, "posterior_prob": 0.0001, "msa_time_ms": 119510, "modeltest_time_ms": 12813, "tree_mcmc_time_ms": 4320, "total_cpu_time_ms": 136643 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT v7.526 -> *IQ-TREE v2.4.0 -> *LSD2 v2.4.4 -> *BEAST v1.10.4 -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10)", "chain_rank_in_regime": 7, "global_rank": 28, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (K80+G4) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10", "model_name": "K80+G4", "k_free_params": 127, "marginal_ln_l": -480518.5878, "delta_ln_l_vs_best": -138517.732, "aic": 961291.1756, "bic": 962331.6128, "rcfv": 0.0371, "bootstrap_support_pct": 98.2, "posterior_prob": 0.9991, "msa_time_ms": 119510, "modeltest_time_ms": 9891, "tree_mcmc_time_ms": 4320, "total_cpu_time_ms": 133721 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unrecoded Saturation + Unfiltered NUMT Pseudogene Chimera)", "chain_rank_in_regime": 7, "global_rank": 29, "tool_chain_summary": "Raw Uncleaned Supermatrix -> No RY3 / No NUMT Chimera Filter -> *IQ-TREE v2.4.0 (K80+G4) -> Uncleaned Skyline (0-Beaker Rejected)", "model_name": "K80+G4", "k_free_params": 127, "marginal_ln_l": -488051.0418, "delta_ln_l_vs_best": -146050.186, "aic": 976356.0836, "bic": 977396.5208, "rcfv": 0.0407, "bootstrap_support_pct": 59.4, "posterior_prob": 0.0001, "msa_time_ms": 119510, "modeltest_time_ms": 10344, "tree_mcmc_time_ms": 4320, "total_cpu_time_ms": 134174 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (super-blast -> *MAFFT v7.526 -> popgen-blind-dualpass [RY3] -> *IQ-TREE v2.4.0 -> *LSD2 -> runie-mcmc-skyline -> *PAML v4.10.10)", "chain_rank_in_regime": 8, "global_rank": 30, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (JC) -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "JC", "k_free_params": 125, "marginal_ln_l": -489730.5803, "delta_ln_l_vs_best": -147729.7245, "aic": 979711.1605, "bic": 980735.2129, "rcfv": 0.007, "bootstrap_support_pct": 100, "posterior_prob": 1, "msa_time_ms": 119510, "modeltest_time_ms": 2031, "tree_mcmc_time_ms": 2980, "total_cpu_time_ms": 124521 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT v7.526 -> *IQ-TREE v2.4.0 -> *LSD2 v2.4.4 -> *BEAST v1.10.4 -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10)", "chain_rank_in_regime": 8, "global_rank": 31, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (JC) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10", "model_name": "JC", "k_free_params": 125, "marginal_ln_l": -585006.9884, "delta_ln_l_vs_best": -243006.1326, "aic": 1170263.9768, "bic": 1171288.0291, "rcfv": 0.0371, "bootstrap_support_pct": 98.2, "posterior_prob": 0.9991, "msa_time_ms": 119510, "modeltest_time_ms": 2203, "tree_mcmc_time_ms": 4320, "total_cpu_time_ms": 126033 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unrecoded Saturation + Unfiltered NUMT Pseudogene Chimera)", "chain_rank_in_regime": 8, "global_rank": 32, "tool_chain_summary": "Raw Uncleaned Supermatrix -> No RY3 / No NUMT Chimera Filter -> *IQ-TREE v2.4.0 (JC) -> Uncleaned Skyline (0-Beaker Rejected)", "model_name": "JC", "k_free_params": 125, "marginal_ln_l": -591888.7504, "delta_ln_l_vs_best": -249887.8946, "aic": 1184027.5009, "bic": 1185051.5532, "rcfv": 0.0407, "bootstrap_support_pct": 59.4, "posterior_prob": 0.0001, "msa_time_ms": 119510, "modeltest_time_ms": 1891, "tree_mcmc_time_ms": 4320, "total_cpu_time_ms": 125721 } ], "core_taxa_manifest": [ { "id": "T001", "sector": "A", "clade": "Lagomorpha (Outgroup)", "guild": "Duplex-incisor browser/grazer & lagomorph vector-host baseline", "acc": "NC_088544.1", "species": "Lepus mandshuricus", "len": 16705, "gcPct": 38.89, "sha256": "b8bc2f7c0e4ae732", "file": "val_set_059_rodents/mito_T001_NC_088544.1.fasta" }, { "id": "T002", "sector": "A", "clade": "Lagomorpha (Outgroup)", "guild": "Duplex-incisor browser/grazer & lagomorph vector-host baseline", "acc": "NC_086490.1", "species": "Ochotona rufescens", "len": 16408, "gcPct": 43.97, "sha256": "93708aa091c789de", "file": "val_set_059_rodents/mito_T002_NC_086490.1.fasta" }, { "id": "T003", "sector": "A", "clade": "Lagomorpha (Outgroup)", "guild": "Duplex-incisor browser/grazer & lagomorph vector-host baseline", "acc": "NC_084122.1", "species": "Ochotona pallasi pricei", "len": 16954, "gcPct": 43.18, "sha256": "8221e183f2fecd79", "file": "val_set_059_rodents/mito_T003_NC_084122.1.fasta" }, { "id": "T004", "sector": "A", "clade": "Lagomorpha (Outgroup)", "guild": "Duplex-incisor browser/grazer & lagomorph vector-host baseline", "acc": "NC_065133.1", "species": "Lepus tibetanus", "len": 16809, "gcPct": 39.01, "sha256": "b060f54f6725a7cd", "file": "val_set_059_rodents/mito_T004_NC_065133.1.fasta" }, { "id": "T005", "sector": "B", "clade": "Sciuromorpha (Sciuridae & Aplodontiidae)", "guild": "Fossorial colonial grassland engineers & arboreal granivores; sylvatic plague (Yersinia pestis) & tick virus amplification", "acc": "NC_086593.1", "species": "Marmota sibirica", "len": 16437, "gcPct": 36.16, "sha256": "039444acd1b2c446", "file": "val_set_059_rodents/mito_T005_NC_086593.1.fasta" }, { "id": "T006", "sector": "B", "clade": "Sciuromorpha (Sciuridae & Aplodontiidae)", "guild": "Fossorial colonial grassland engineers & arboreal granivores; sylvatic plague (Yersinia pestis) & tick virus 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"sector": "B", "clade": "Sciuromorpha (Sciuridae & Aplodontiidae)", "guild": "Fossorial colonial grassland engineers & arboreal granivores; sylvatic plague (Yersinia pestis) & tick virus amplification", "acc": "NC_050033.1", "species": "Sciurus lis", "len": 16512, "gcPct": 36.91, "sha256": "619044346df338cb", "file": "val_set_059_rodents/mito_T009_NC_050033.1.fasta" }, { "id": "T010", "sector": "B", "clade": "Sciuromorpha (Sciuridae & Aplodontiidae)", "guild": "Fossorial colonial grassland engineers & arboreal granivores; sylvatic plague (Yersinia pestis) & tick virus amplification", "acc": "NC_050032.1", "species": "Sciurus ignitus", "len": 16519, "gcPct": 38.14, "sha256": "35329801541da50b", "file": "val_set_059_rodents/mito_T010_NC_050032.1.fasta" }, { "id": "T011", "sector": "B", "clade": "Sciuromorpha (Sciuridae & Aplodontiidae)", "guild": "Fossorial colonial grassland engineers & arboreal granivores; sylvatic plague (Yersinia pestis) & tick virus amplification", "acc": 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"clade": "Sciuromorpha (Sciuridae & Aplodontiidae)", "guild": "Fossorial colonial grassland engineers & arboreal granivores; sylvatic plague (Yersinia pestis) & tick virus amplification", "acc": "NC_050024.1", "species": "Simosciurus stramineus", "len": 16512, "gcPct": 38.03, "sha256": "6814a8d661f4dc1d", "file": "val_set_059_rodents/mito_T014_NC_050024.1.fasta" }, { "id": "T015", "sector": "B", "clade": "Sciuromorpha (Sciuridae & Aplodontiidae)", "guild": "Fossorial colonial grassland engineers & arboreal granivores; sylvatic plague (Yersinia pestis) & tick virus amplification", "acc": "NC_050018.1", "species": "Sciurus granatensis", "len": 16515, "gcPct": 37.66, "sha256": "2a52aec569ee5cfb", "file": "val_set_059_rodents/mito_T015_NC_050018.1.fasta" }, { "id": "T016", "sector": "C", "clade": "Castorimorpha & Anomaluromorpha (Castoridae, Geomyidae, Heteromyidae & Pedetidae)", "guild": "Riparian dam-builders (Castor), fossorial pocket gophers (Geomys/Thomomys) & arid desert kangaroo 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"CM139418.1", "species": "Castor canadensis", "len": 16714, "gcPct": 41.7, "sha256": "38f05247858b033b", "file": "val_set_059_rodents/mito_T018_CM139418.1.fasta" }, { "id": "T019", "sector": "C", "clade": "Castorimorpha & Anomaluromorpha (Castoridae, Geomyidae, Heteromyidae & Pedetidae)", "guild": "Riparian dam-builders (Castor), fossorial pocket gophers (Geomys/Thomomys) & arid desert kangaroo rats (Dipodomys); Giardia & Coccidioides soil reservoirs", "acc": "PQ325572.1", "species": "Castor fiber subsp.", "len": 17002, "gcPct": 40.65, "sha256": "caf1a3a1abfca799", "file": "val_set_059_rodents/mito_T019_PQ325572.1.fasta" }, { "id": "T020", "sector": "C", "clade": "Castorimorpha & Anomaluromorpha (Castoridae, Geomyidae, Heteromyidae & Pedetidae)", "guild": "Riparian dam-builders (Castor), fossorial pocket gophers (Geomys/Thomomys) & arid desert kangaroo rats (Dipodomys); Giardia & Coccidioides soil reservoirs", "acc": "CM063266.1", "species": "Perognathus longimembris", "len": 16962, "gcPct": 34.36, "sha256": "fec577acce7fe3d7", "file": "val_set_059_rodents/mito_T020_CM063266.1.fasta" }, { "id": "T021", "sector": "C", "clade": "Castorimorpha & Anomaluromorpha (Castoridae, Geomyidae, Heteromyidae & Pedetidae)", "guild": "Riparian dam-builders (Castor), fossorial pocket gophers (Geomys/Thomomys) & arid desert kangaroo rats (Dipodomys); Giardia & Coccidioides soil reservoirs", "acc": "CM063115.1", "species": "Thomomys bottae", "len": 17079, "gcPct": 34.5, "sha256": "ea379d8d24f57b26", "file": "val_set_059_rodents/mito_T021_CM063115.1.fasta" }, { "id": "T022", "sector": "C", "clade": "Castorimorpha & Anomaluromorpha (Castoridae, Geomyidae, Heteromyidae & Pedetidae)", "guild": "Riparian dam-builders (Castor), fossorial pocket gophers (Geomys/Thomomys) & arid desert kangaroo rats (Dipodomys); Giardia & Coccidioides soil reservoirs", "acc": "NC_069016.1", "species": "Geomys pinetis", "len": 16857, "gcPct": 35.45, "sha256": "4f83b0dce1406945", "file": "val_set_059_rodents/mito_T022_NC_069016.1.fasta" }, { "id": "T023", "sector": "C", "clade": "Castorimorpha & Anomaluromorpha (Castoridae, Geomyidae, Heteromyidae & Pedetidae)", "guild": "Riparian dam-builders (Castor), fossorial pocket gophers (Geomys/Thomomys) & arid desert kangaroo rats (Dipodomys); Giardia & Coccidioides soil reservoirs", "acc": "NC_068810.1", "species": "Chaetodipus penicillatus", "len": 16332, "gcPct": 37.62, "sha256": "71094e4ea57ef3e0", "file": "val_set_059_rodents/mito_T023_NC_068810.1.fasta" }, { "id": "T024", "sector": "C", "clade": "Castorimorpha & Anomaluromorpha (Castoridae, Geomyidae, Heteromyidae & Pedetidae)", "guild": "Riparian dam-builders (Castor), fossorial pocket gophers (Geomys/Thomomys) & arid desert kangaroo rats (Dipodomys); Giardia & Coccidioides soil reservoirs", "acc": "NC_068808.1", "species": "Dipodomys spectabilis", "len": 16270, "gcPct": 39.31, "sha256": "2f4d39e5556559a5", "file": "val_set_059_rodents/mito_T024_NC_068808.1.fasta" }, { "id": "T025", "sector": "C", "clade": "Castorimorpha & Anomaluromorpha (Castoridae, Geomyidae, Heteromyidae & Pedetidae)", "guild": "Riparian dam-builders (Castor), fossorial pocket gophers (Geomys/Thomomys) & arid desert kangaroo rats (Dipodomys); Giardia & Coccidioides soil reservoirs", "acc": "NC_068807.1", "species": "Dipodomys merriami", "len": 16260, "gcPct": 38.15, "sha256": "675ebf0a2e2d1b96", "file": "val_set_059_rodents/mito_T025_NC_068807.1.fasta" }, { "id": "T026", "sector": "D", "clade": "Cricetidae: Neotominae (Deer Mice & Woodrats)", "guild": "North American forest/arid generalists (Peromyscus & Neotoma); primary Sin Nombre orthohantavirus (SNV) & Borrelia burgdorferi Lyme disease reservoirs", "acc": "PZ213497.1", "species": "Peromyscus truei", "len": 16539, "gcPct": 35.7, "sha256": "347485b1578bb19c", "file": "val_set_059_rodents/mito_T026_PZ213497.1.fasta" }, { "id": "T027", "sector": "D", "clade": "Cricetidae: Neotominae (Deer Mice & Woodrats)", "guild": "North American forest/arid generalists (Peromyscus & Neotoma); primary Sin Nombre orthohantavirus (SNV) & Borrelia burgdorferi Lyme disease reservoirs", "acc": "PZ213495.1", "species": "Peromyscus gambelii clementis", "len": 16325, "gcPct": 36.62, "sha256": "7a9c5bc7d28f34d2", "file": "val_set_059_rodents/mito_T027_PZ213495.1.fasta" }, { "id": "T028", "sector": "D", "clade": "Cricetidae: Neotominae (Deer Mice & Woodrats)", "guild": "North American forest/arid generalists (Peromyscus & Neotoma); primary Sin Nombre orthohantavirus (SNV) & Borrelia burgdorferi Lyme disease reservoirs", "acc": "PP818785.1", "species": "Reithrodontomys tenuirostris", "len": 16609, "gcPct": 37.67, "sha256": "dd8cc418aed7a5f7", "file": "val_set_059_rodents/mito_T028_PP818785.1.fasta" }, { "id": "T029", "sector": "D", "clade": "Cricetidae: Neotominae (Deer Mice & Woodrats)", "guild": "North American forest/arid generalists (Peromyscus & Neotoma); primary Sin Nombre orthohantavirus (SNV) & Borrelia burgdorferi Lyme 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"f02c6c147f789430", "file": "val_set_059_rodents/mito_T031_PP818782.1.fasta" }, { "id": "T032", "sector": "D", "clade": "Cricetidae: Neotominae (Deer Mice & Woodrats)", "guild": "North American forest/arid generalists (Peromyscus & Neotoma); primary Sin Nombre orthohantavirus (SNV) & Borrelia burgdorferi Lyme disease reservoirs", "acc": "PP818781.1", "species": "Reithrodontomys humulis", "len": 16489, "gcPct": 34.51, "sha256": "12750fb3aead3922", "file": "val_set_059_rodents/mito_T032_PP818781.1.fasta" }, { "id": "T033", "sector": "D", "clade": "Cricetidae: Neotominae (Deer Mice & Woodrats)", "guild": "North American forest/arid generalists (Peromyscus & Neotoma); primary Sin Nombre orthohantavirus (SNV) & Borrelia burgdorferi Lyme disease reservoirs", "acc": "PP818780.1", "species": "Reithrodontomys fulvescens", "len": 16612, "gcPct": 34.55, "sha256": "27c59460ecfc2371", "file": "val_set_059_rodents/mito_T033_PP818780.1.fasta" }, { "id": "T034", "sector": "D", "clade": "Cricetidae: Neotominae (Deer Mice & Woodrats)", "guild": "North American forest/arid generalists (Peromyscus & Neotoma); primary Sin Nombre orthohantavirus (SNV) & Borrelia burgdorferi Lyme disease reservoirs", "acc": "PP818779.1", "species": "Peromyscus zarhynchus", "len": 16428, "gcPct": 37.72, "sha256": "b30bce4116bafeb9", "file": "val_set_059_rodents/mito_T034_PP818779.1.fasta" }, { "id": "T035", "sector": "D", "clade": "Cricetidae: Neotominae (Deer Mice & Woodrats)", "guild": "North American forest/arid generalists (Peromyscus & Neotoma); primary Sin Nombre orthohantavirus (SNV) & Borrelia burgdorferi Lyme disease reservoirs", "acc": "PP818777.1", "species": "Peromyscus spicilegus", "len": 16636, "gcPct": 37.6, "sha256": "7b3baca69c25736c", "file": "val_set_059_rodents/mito_T035_PP818777.1.fasta" }, { "id": "T036", "sector": "D", "clade": "Cricetidae: Neotominae (Deer Mice & Woodrats)", "guild": "North American forest/arid generalists (Peromyscus & Neotoma); primary Sin Nombre orthohantavirus 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"NM_001271074.1", "species": "Rattus norvegicus amelogenin,", "len": 808, "gcPct": 54.33, "sha256": "2ade2291260cc8cc", "file": "val_set_059_rodents/nuc_NUC31_NM_001271074.1.fasta" }, { "recId": "NUC32", "familyKey": "ENAM_AMELX_Hypsodont", "familyLabel": "ENAM Dental Enamelin & AMELX Amelogenin Incisor/Hypsodont Matrix", "funcNote": "Reinforces iron-pigmented ever-growing chisel incisors in Castor/Geomys/Erethizon and prismatic hypsodont grazing molars in Microtus and Sigmodon", "acc": "NM_001271073.1", "species": "Rattus norvegicus amelogenin,", "len": 736, "gcPct": 54.62, "sha256": "c802aad9928d9cf6", "file": "val_set_059_rodents/nuc_NUC32_NM_001271073.1.fasta" }, { "recId": "NUC33", "familyKey": "IGHG_MHC_Zoonotic_Immunity", "familyLabel": "FCGRT / MHC-II Zoonotic Reservoir Persistent Viral & Spirochete Tolerance Complex", "funcNote": "Modulates non-cytopathic persistent orthohantavirus and Borrelia spirochete carriage without immunopathological cytokine storm in Peromyscus and 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