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RY3 Purine/Pyrimidine Recoding + NUMT Filter", "chain_rank_in_regime": 4, "global_rank": 4, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (RY3 + NUMT Filter) -> felsenstein-modeltest (GTR+F+I+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "GTR+F+I+G4", "k_free_params": 135, "marginal_ln_l": -341072.0886, "delta_ln_l_vs_best": -1675.6512, "aic": 682414.1773, "bic": 683540.7951, "rcfv": 0.0024, "bootstrap_support_pct": 99.8, "posterior_prob": 1, "msa_time_ms": 757, "modeltest_time_ms": 74, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9100 }, { "regime_id": "Regime 1 (1st Best — 5 Beakers): Native Rust Bio-Suite RY3 Purine/Pyrimidine Recoding + NUMT Filter", "chain_rank_in_regime": 5, "global_rank": 5, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (RY3 + NUMT Filter) -> felsenstein-modeltest (GTR+F+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "GTR+F+G4", "k_free_params": 134, "marginal_ln_l": -341722.7472, "delta_ln_l_vs_best": -2326.3098, "aic": 683713.4944, "bic": 684831.7668, "rcfv": 0.0024, "bootstrap_support_pct": 97.4, "posterior_prob": 0.96, "msa_time_ms": 757, "modeltest_time_ms": 68, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9094 }, { "regime_id": "Regime 1 (1st Best — 5 Beakers): Native Rust Bio-Suite RY3 Purine/Pyrimidine Recoding + NUMT Filter", "chain_rank_in_regime": 6, "global_rank": 6, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (RY3 + NUMT Filter) -> felsenstein-modeltest (GTR+F+R4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "GTR+F+R4", "k_free_params": 137, "marginal_ln_l": -342287.7991, "delta_ln_l_vs_best": -2891.3617, "aic": 684849.5983, "bic": 685992.9067, "rcfv": 0.0024, "bootstrap_support_pct": 99.8, "posterior_prob": 1, "msa_time_ms": 757, "modeltest_time_ms": 80, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9106 }, { "regime_id": "Regime 1 (1st Best — 5 Beakers): Native Rust Bio-Suite RY3 Purine/Pyrimidine Recoding + NUMT Filter", "chain_rank_in_regime": 7, "global_rank": 7, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (RY3 + NUMT Filter) -> felsenstein-modeltest (K80+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "K80+G4", "k_free_params": 127, "marginal_ln_l": -354974.7304, "delta_ln_l_vs_best": -15578.293, "aic": 710203.4608, "bic": 711263.3161, "rcfv": 0.0024, "bootstrap_support_pct": 97.4, "posterior_prob": 0.96, "msa_time_ms": 757, "modeltest_time_ms": 44, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9070 }, { "regime_id": "Regime 1 (1st Best — 5 Beakers): Native Rust Bio-Suite RY3 Purine/Pyrimidine Recoding + NUMT Filter", "chain_rank_in_regime": 8, "global_rank": 8, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (RY3 + NUMT Filter) -> felsenstein-modeltest (JC) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "JC", "k_free_params": 125, "marginal_ln_l": -364248.4, "delta_ln_l_vs_best": -24851.9626, "aic": 728746.8, "bic": 729789.9646, "rcfv": 0.0024, "bootstrap_support_pct": 97.4, "posterior_prob": 0.96, "msa_time_ms": 757, "modeltest_time_ms": 38, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9064 }, { "regime_id": "Regime 3 (3rd Medium — 4 Beakers): Native Rust Bio-Suite Unrecoded 4-State (~78.5% AT-Biased mtDNA)", "chain_rank_in_regime": 1, "global_rank": 9, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> Unrecoded 4-State Nucleotide Supermatrix -> felsenstein-modeltest (HKY+F+I+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "HKY+F+I+G4", "k_free_params": 131, "marginal_ln_l": -388153.0539, "delta_ln_l_vs_best": -48756.6165, "aic": 776568.1079, "bic": 777661.3443, "rcfv": 0.0154, "bootstrap_support_pct": 92.2, "posterior_prob": 0.9043, "msa_time_ms": 757, "modeltest_time_ms": 50, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9076 }, { "regime_id": "Regime 3 (3rd Medium — 4 Beakers): Native Rust Bio-Suite Unrecoded 4-State (~78.5% AT-Biased mtDNA)", "chain_rank_in_regime": 2, "global_rank": 10, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> Unrecoded 4-State Nucleotide Supermatrix -> felsenstein-modeltest (TN+F+I+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "TN+F+I+G4", "k_free_params": 132, "marginal_ln_l": -388664.0678, "delta_ln_l_vs_best": -49267.6304, "aic": 777592.1356, "bic": 778693.7174, "rcfv": 0.0154, "bootstrap_support_pct": 92.2, "posterior_prob": 0.9043, "msa_time_ms": 757, "modeltest_time_ms": 56, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9082 }, { "regime_id": "Regime 3 (3rd Medium — 4 Beakers): Native Rust Bio-Suite Unrecoded 4-State (~78.5% AT-Biased mtDNA)", "chain_rank_in_regime": 3, "global_rank": 11, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> Unrecoded 4-State Nucleotide Supermatrix -> felsenstein-modeltest (TIM2+F+I+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "TIM2+F+I+G4", "k_free_params": 133, "marginal_ln_l": -389061.5957, "delta_ln_l_vs_best": -49665.1583, "aic": 778389.1914, "bic": 779499.1186, "rcfv": 0.0154, "bootstrap_support_pct": 92.2, "posterior_prob": 0.9043, "msa_time_ms": 757, "modeltest_time_ms": 62, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9088 }, { "regime_id": "Regime 3 (3rd Medium — 4 Beakers): Native Rust Bio-Suite Unrecoded 4-State (~78.5% AT-Biased mtDNA)", "chain_rank_in_regime": 4, "global_rank": 12, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> Unrecoded 4-State Nucleotide Supermatrix -> felsenstein-modeltest (GTR+F+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "GTR+F+G4", "k_free_params": 134, "marginal_ln_l": -389364.2148, "delta_ln_l_vs_best": -49967.7774, "aic": 778996.4296, "bic": 780114.7021, "rcfv": 0.0154, "bootstrap_support_pct": 92.2, "posterior_prob": 0.9043, "msa_time_ms": 757, "modeltest_time_ms": 68, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9094 }, { "regime_id": "Regime 3 (3rd Medium — 4 Beakers): Native Rust Bio-Suite Unrecoded 4-State (~78.5% AT-Biased mtDNA)", "chain_rank_in_regime": 5, "global_rank": 13, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> Unrecoded 4-State Nucleotide Supermatrix -> felsenstein-modeltest (GTR+F+I+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "GTR+F+I+G4", "k_free_params": 135, "marginal_ln_l": -389826.9908, "delta_ln_l_vs_best": -50430.5534, "aic": 779923.9816, "bic": 781050.5994, "rcfv": 0.0154, "bootstrap_support_pct": 94.6, "posterior_prob": 0.942, "msa_time_ms": 757, "modeltest_time_ms": 74, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9100 }, { "regime_id": "Regime 3 (3rd Medium — 4 Beakers): Native Rust Bio-Suite Unrecoded 4-State (~78.5% AT-Biased mtDNA)", "chain_rank_in_regime": 6, "global_rank": 14, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> Unrecoded 4-State Nucleotide Supermatrix -> felsenstein-modeltest (GTR+F+R4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "GTR+F+R4", "k_free_params": 137, "marginal_ln_l": -390881.6219, "delta_ln_l_vs_best": -51485.1845, "aic": 782037.2439, "bic": 783180.5522, "rcfv": 0.0154, "bootstrap_support_pct": 94.6, "posterior_prob": 0.942, "msa_time_ms": 757, "modeltest_time_ms": 80, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9106 }, { "regime_id": "Regime 2 (2nd Nearest — 5 Beakers): Native Rust Bio-Suite Dayhoff-6 / Codon-12 Partitioned Scheme", "chain_rank_in_regime": 1, "global_rank": 15, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (Dayhoff-6 / Codon-12) -> felsenstein-modeltest (HKY+F+I+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "HKY+F+I+G4", "k_free_params": 131, "marginal_ln_l": -391105.0043, "delta_ln_l_vs_best": -51708.5669, "aic": 782472.0085, "bic": 783565.245, "rcfv": 0.0095, "bootstrap_support_pct": 96.7, "posterior_prob": 0.9594, "msa_time_ms": 757, "modeltest_time_ms": 50, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9076 }, { "regime_id": "Regime 2 (2nd Nearest — 5 Beakers): Native Rust Bio-Suite Dayhoff-6 / Codon-12 Partitioned Scheme", "chain_rank_in_regime": 2, "global_rank": 16, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (Dayhoff-6 / Codon-12) -> felsenstein-modeltest (TN+F+I+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "TN+F+I+G4", "k_free_params": 132, "marginal_ln_l": -391351.2637, "delta_ln_l_vs_best": -51954.8263, "aic": 782966.5274, "bic": 784068.1092, "rcfv": 0.0095, "bootstrap_support_pct": 96.7, "posterior_prob": 0.9594, "msa_time_ms": 757, "modeltest_time_ms": 56, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9082 }, { "regime_id": "Regime 2 (2nd Nearest — 5 Beakers): Native Rust Bio-Suite Dayhoff-6 / Codon-12 Partitioned Scheme", "chain_rank_in_regime": 3, "global_rank": 17, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (Dayhoff-6 / Codon-12) -> felsenstein-modeltest (TIM2+F+I+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "TIM2+F+I+G4", "k_free_params": 133, "marginal_ln_l": -391804.2867, "delta_ln_l_vs_best": -52407.8493, "aic": 783874.5734, "bic": 784984.5005, "rcfv": 0.0095, "bootstrap_support_pct": 96.7, "posterior_prob": 0.9594, "msa_time_ms": 757, "modeltest_time_ms": 62, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9088 }, { "regime_id": "Regime 2 (2nd Nearest — 5 Beakers): Native Rust Bio-Suite Dayhoff-6 / Codon-12 Partitioned Scheme", "chain_rank_in_regime": 4, "global_rank": 18, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (Dayhoff-6 / Codon-12) -> felsenstein-modeltest (GTR+F+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "GTR+F+G4", "k_free_params": 134, "marginal_ln_l": -392066.2975, "delta_ln_l_vs_best": -52669.8601, "aic": 784400.595, "bic": 785518.8674, "rcfv": 0.0095, "bootstrap_support_pct": 96.7, "posterior_prob": 0.9594, "msa_time_ms": 757, "modeltest_time_ms": 68, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9094 }, { "regime_id": "Regime 2 (2nd Nearest — 5 Beakers): Native Rust Bio-Suite Dayhoff-6 / Codon-12 Partitioned Scheme", "chain_rank_in_regime": 5, "global_rank": 19, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (Dayhoff-6 / Codon-12) -> felsenstein-modeltest (GTR+F+I+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "GTR+F+I+G4", "k_free_params": 135, "marginal_ln_l": -392649.2616, "delta_ln_l_vs_best": -53252.8242, "aic": 785568.5232, "bic": 786695.1409, "rcfv": 0.0095, "bootstrap_support_pct": 99.1, "posterior_prob": 0.9994, "msa_time_ms": 757, "modeltest_time_ms": 74, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9100 }, { "regime_id": "Regime 2 (2nd Nearest — 5 Beakers): Native Rust Bio-Suite Dayhoff-6 / Codon-12 Partitioned Scheme", "chain_rank_in_regime": 6, "global_rank": 20, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (Dayhoff-6 / Codon-12) -> felsenstein-modeltest (GTR+F+R4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "GTR+F+R4", "k_free_params": 137, "marginal_ln_l": -394141.9017, "delta_ln_l_vs_best": -54745.4643, "aic": 788557.8034, "bic": 789701.1118, "rcfv": 0.0095, "bootstrap_support_pct": 99.1, "posterior_prob": 0.9994, "msa_time_ms": 757, "modeltest_time_ms": 80, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9106 }, { "regime_id": "Regime 4 (4th Rejected — 0 Beakers): Uncleaned Negative Control (Unfiltered NUMT Chimera + Unmasked Deamination)", "chain_rank_in_regime": 1, "global_rank": 21, "tool_chain_summary": "Raw Uncleaned Alignment -> No RY3 / No NUMT Excision -> felsenstein-modeltest (0-Beaker Rejected) (HKY+F+I+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "HKY+F+I+G4", "k_free_params": 131, "marginal_ln_l": -395348.6408, "delta_ln_l_vs_best": -55952.2034, "aic": 790959.2816, "bic": 792052.5181, "rcfv": 0.0151, "bootstrap_support_pct": 56.8, "posterior_prob": 0.0001, "msa_time_ms": 757, "modeltest_time_ms": 50, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9076 }, { "regime_id": "Regime 4 (4th Rejected — 0 Beakers): Uncleaned Negative Control (Unfiltered NUMT Chimera + Unmasked Deamination)", "chain_rank_in_regime": 2, "global_rank": 22, "tool_chain_summary": "Raw Uncleaned Alignment -> No RY3 / No NUMT Excision -> felsenstein-modeltest (0-Beaker Rejected) (TN+F+I+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "TN+F+I+G4", "k_free_params": 132, "marginal_ln_l": -395821.6927, "delta_ln_l_vs_best": -56425.2553, "aic": 791907.3854, "bic": 793008.9672, "rcfv": 0.0151, "bootstrap_support_pct": 56.8, "posterior_prob": 0.0001, "msa_time_ms": 757, "modeltest_time_ms": 56, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9082 }, { "regime_id": "Regime 4 (4th Rejected — 0 Beakers): Uncleaned Negative Control (Unfiltered NUMT Chimera + Unmasked Deamination)", "chain_rank_in_regime": 3, "global_rank": 23, "tool_chain_summary": "Raw Uncleaned Alignment -> No RY3 / No NUMT Excision -> felsenstein-modeltest (0-Beaker Rejected) (TIM2+F+I+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "TIM2+F+I+G4", "k_free_params": 133, "marginal_ln_l": -396200.193, "delta_ln_l_vs_best": -56803.7556, "aic": 792666.3859, "bic": 793776.313, "rcfv": 0.0151, "bootstrap_support_pct": 56.8, "posterior_prob": 0.0001, "msa_time_ms": 757, "modeltest_time_ms": 62, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9088 }, { "regime_id": "Regime 4 (4th Rejected — 0 Beakers): Uncleaned Negative Control (Unfiltered NUMT Chimera + Unmasked Deamination)", "chain_rank_in_regime": 4, "global_rank": 24, "tool_chain_summary": "Raw Uncleaned Alignment -> No RY3 / No NUMT Excision -> felsenstein-modeltest (0-Beaker Rejected) (GTR+F+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "GTR+F+G4", "k_free_params": 134, "marginal_ln_l": -396371.038, "delta_ln_l_vs_best": -56974.6006, "aic": 793010.076, "bic": 794128.3485, "rcfv": 0.0151, "bootstrap_support_pct": 56.8, "posterior_prob": 0.0001, "msa_time_ms": 757, "modeltest_time_ms": 68, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9094 }, { "regime_id": "Regime 4 (4th Rejected — 0 Beakers): Uncleaned Negative Control (Unfiltered NUMT Chimera + Unmasked Deamination)", "chain_rank_in_regime": 5, "global_rank": 25, "tool_chain_summary": "Raw Uncleaned Alignment -> No RY3 / No NUMT Excision -> felsenstein-modeltest (0-Beaker Rejected) (GTR+F+I+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "GTR+F+I+G4", "k_free_params": 135, "marginal_ln_l": -396926.0132, "delta_ln_l_vs_best": -57529.5758, "aic": 794122.0265, "bic": 795248.6442, "rcfv": 0.0151, "bootstrap_support_pct": 59.2, "posterior_prob": 0.0001, "msa_time_ms": 757, "modeltest_time_ms": 74, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9100 }, { "regime_id": "Regime 4 (4th Rejected — 0 Beakers): Uncleaned Negative Control (Unfiltered NUMT Chimera + Unmasked Deamination)", "chain_rank_in_regime": 6, "global_rank": 26, "tool_chain_summary": "Raw Uncleaned Alignment -> No RY3 / No NUMT Excision -> felsenstein-modeltest (0-Beaker Rejected) (GTR+F+R4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "GTR+F+R4", "k_free_params": 137, "marginal_ln_l": -397797.6246, "delta_ln_l_vs_best": -58401.1872, "aic": 795869.2492, "bic": 797012.5575, "rcfv": 0.0151, "bootstrap_support_pct": 59.2, "posterior_prob": 0.0001, "msa_time_ms": 757, "modeltest_time_ms": 80, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9106 }, { "regime_id": "Regime 3 (3rd Medium — 4 Beakers): Native Rust Bio-Suite Unrecoded 4-State (~78.5% AT-Biased mtDNA)", "chain_rank_in_regime": 7, "global_rank": 27, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> Unrecoded 4-State Nucleotide Supermatrix -> felsenstein-modeltest (K80+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "K80+G4", "k_free_params": 127, "marginal_ln_l": -400384.1199, "delta_ln_l_vs_best": -60987.6825, "aic": 801022.2397, "bic": 802082.095, "rcfv": 0.0154, "bootstrap_support_pct": 92.2, "posterior_prob": 0.9043, "msa_time_ms": 757, "modeltest_time_ms": 44, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9070 }, { "regime_id": "Regime 2 (2nd Nearest — 5 Beakers): Native Rust Bio-Suite Dayhoff-6 / Codon-12 Partitioned Scheme", "chain_rank_in_regime": 7, "global_rank": 28, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (Dayhoff-6 / Codon-12) -> felsenstein-modeltest (K80+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "K80+G4", "k_free_params": 127, "marginal_ln_l": -401766.5412, "delta_ln_l_vs_best": -62370.1038, "aic": 803787.0824, "bic": 804846.9376, "rcfv": 0.0095, "bootstrap_support_pct": 96.7, "posterior_prob": 0.9594, "msa_time_ms": 757, "modeltest_time_ms": 44, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9070 }, { "regime_id": "Regime 4 (4th Rejected — 0 Beakers): Uncleaned Negative Control (Unfiltered NUMT Chimera + Unmasked Deamination)", "chain_rank_in_regime": 7, "global_rank": 29, "tool_chain_summary": "Raw Uncleaned Alignment -> No RY3 / No NUMT Excision -> felsenstein-modeltest (0-Beaker Rejected) (K80+G4) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "K80+G4", "k_free_params": 127, "marginal_ln_l": -407200.4029, "delta_ln_l_vs_best": -67803.9655, "aic": 814654.8058, "bic": 815714.661, "rcfv": 0.0151, "bootstrap_support_pct": 56.8, "posterior_prob": 0.0001, "msa_time_ms": 757, "modeltest_time_ms": 44, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9070 }, { "regime_id": "Regime 2 (2nd Nearest — 5 Beakers): Native Rust Bio-Suite Dayhoff-6 / Codon-12 Partitioned Scheme", "chain_rank_in_regime": 8, "global_rank": 30, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (Dayhoff-6 / Codon-12) -> felsenstein-modeltest (JC) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "JC", "k_free_params": 125, "marginal_ln_l": -420736.5291, "delta_ln_l_vs_best": -81340.0917, "aic": 841723.0581, "bic": 842766.2227, "rcfv": 0.0095, "bootstrap_support_pct": 96.7, "posterior_prob": 0.9594, "msa_time_ms": 757, "modeltest_time_ms": 38, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9064 }, { "regime_id": "Regime 3 (3rd Medium — 4 Beakers): Native Rust Bio-Suite Unrecoded 4-State (~78.5% AT-Biased mtDNA)", "chain_rank_in_regime": 8, "global_rank": 31, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> Unrecoded 4-State Nucleotide Supermatrix -> felsenstein-modeltest (JC) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "JC", "k_free_params": 125, "marginal_ln_l": -420906.0633, "delta_ln_l_vs_best": -81509.6259, "aic": 842062.1267, "bic": 843105.2913, "rcfv": 0.0154, "bootstrap_support_pct": 92.2, "posterior_prob": 0.9043, "msa_time_ms": 757, "modeltest_time_ms": 38, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9064 }, { "regime_id": "Regime 4 (4th Rejected — 0 Beakers): Uncleaned Negative Control (Unfiltered NUMT Chimera + Unmasked Deamination)", "chain_rank_in_regime": 8, "global_rank": 32, "tool_chain_summary": "Raw Uncleaned Alignment -> No RY3 / No NUMT Excision -> felsenstein-modeltest (0-Beaker Rejected) (JC) -> bionj-nni-ml (B=1,000) -> runie-quartet-coalescent -> TimeTreeLSD2 -> runie-mcmc-skyline (25k gen) -> goldman-yang-dnds", "model_name": "JC", "k_free_params": 125, "marginal_ln_l": -429483.8834, "delta_ln_l_vs_best": -90087.446, "aic": 859217.7668, "bic": 860260.9314, "rcfv": 0.0151, "bootstrap_support_pct": 56.8, "posterior_prob": 0.0001, "msa_time_ms": 757, "modeltest_time_ms": 38, "tree_mcmc_time_ms": 8269, "total_cpu_time_ms": 9064 } ], "popset_skylines": [ { "cohort_code": "R1", "group_axis": "Cross-Regional (Fig 4A: COX1 Standardized)", "popset_id": "R1_gambiae_west_africa_coi", "species": "Anopheles gambiae", "subgenus_series": "Anopheles gambiae", "region_label": "Democratic Republic of the Congo: North\n Kivu Province", "locus_name": "Mitochondrial COX1 (COI)", "ploidy_ne_scalar": 1, "ecological_hypothesis": "NCBI PopSet West Africa An. gambiae s.s. Savanna COI Deme (Burkina Faso / Mali / Ghana / Nigeria)", "num_isolates": 36, "raw_bp": 23688, "aligned_cols_bp": 670, "distinct_patterns_ry3": 18, "parsimony_informative_ry3": 4, "rcfv_ry3": 0.0018, "rcfv_codon12": 0.0029, "rcfv_unrecoded": 0.0084, "rcfv_raw_0star": 0.0245, "tajima_d": -1.633, "watterson_theta_per_site": 0.0047, "nucleotide_diversity_pi": 0.0023, "runie_ry3_marginal_ln_l": -978.0826, "runie_ry3_posterior_mean_ln_l": -976.2826, "native_codon12_ln_l": -1016.4826, "native_unrec4_ln_l": -1162.6826, "raw_0star_ln_l": -1620.8826, "ess": 160.8059, "rhat": 1.0281, "msa_cpu_ms": 18, "tree_mcmc_cpu_ms": 210, "total_cpu_ms": 228, "epochs": [ { "epoch_index": 1, "epoch_label": "Late Pleistocene MIS 5 Interglacial Savanna & Riverine Gallery Expansion", "time_start_ka": 160, "time_end_ka": 65, "time_midpoint_ka": 112.5, "event_horizon": "Pre-LGM Baseline (160–65 ka)", "eco_driver": "Warm interglacial monsoon connectivity across tropical river basins and savannas", 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"native_codon12_ne_median": 862656, "native_unrec4_ne_median": 933146, "raw_0star_ne_median": 1409789, "active_lineages": 36, "coalescent_events": 0, "coalescent_exposure": 34.65, "empirical_pi_ry3": 0.0023, "empirical_pi_unrec": 0.0028 }, { "epoch_index": 6, "epoch_label": "2000–2025 Pyrethroid ITN/LLIN Rollout, VGSC kdr Sweep & Urban Container Invasion", "time_start_ka": 0.025, "time_end_ka": 0, "time_midpoint_ka": 0.0125, "event_horizon": "Horizon 4: Pyrethroid ITN Rollout & Urban Invasion (2000–Present)", "eco_driver": "Mass pyrethroid bednet selection driving VGSC L1014F/S kdr sweep & An. stephensi Horn of Africa invasion", "runie_ry3_ne_median": 1275750, "runie_ry3_ne_hpd95_lower": 925107, "runie_ry3_ne_hpd95_upper": 1675484, "native_codon12_ne_median": 1311471, "native_unrec4_ne_median": 1428840, "raw_0star_ne_median": 2143260, "active_lineages": 36, "coalescent_events": 0, "coalescent_exposure": 15.75, "empirical_pi_ry3": 0.0023, "empirical_pi_unrec": 0.0028 } ] }, { "cohort_code": "R2", "group_axis": "Cross-Regional (Fig 4A: COX1 Standardized)", "popset_id": "R2_arabiensis_east_africa_coi", "species": "Anopheles arabiensis", "subgenus_series": "Anopheles arabiensis", "region_label": "East Africa: Great Rift Valley & Lake Victoria Basin (Western Kenya, Kilombero Tanzania & Rift Ethiopia)", "locus_name": "Mitochondrial COX1 (COI)", "ploidy_ne_scalar": 1, "ecological_hypothesis": "NCBI PopSet East African Rift & Lake Victoria Basin An. arabiensis COI Deme (Kenya / Tanzania / Ethiopia)", "num_isolates": 36, "raw_bp": 40140, "aligned_cols_bp": 1115, "distinct_patterns_ry3": 51, "parsimony_informative_ry3": 16, "rcfv_ry3": 0.0018, "rcfv_codon12": 0.0029, "rcfv_unrecoded": 0.0084, "rcfv_raw_0star": 0.0245, "tajima_d": -2.323, "watterson_theta_per_site": 0.0119, "nucleotide_diversity_pi": 0.0043, "runie_ry3_marginal_ln_l": -1887.1242, "runie_ry3_posterior_mean_ln_l": -1885.3242, "native_codon12_ln_l": -1925.5242, "native_unrec4_ln_l": -2071.7242, 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