{ "engine": "bio-suite universal-rp16-supermatrix (candle-core Dayhoff-6/SR4 Recoder + Felsenstein Pruning + Auxotrophy Scanner)", "benchmark_id": "TOOL-BENCHMARK-19-RP16-SUPERMATRIX-VS-IQTREE", "external_reference": "IQ-TREE v2.4.0 (-st AA -m POISSON+FQ and -st MORPH -m MK on Dayhoff-6 & SR4 Recoded Supermatrices)", "total_cohorts": 12, "dev_cohorts": 6, "reserve_cohorts": 6, "dev_mean_aa20_lnl_abs_diff": 0.000034, "reserve_mean_aa20_lnl_abs_diff": 0.000027, "dev_mean_dayhoff6_lnl_abs_diff": 0.000023, "reserve_mean_dayhoff6_lnl_abs_diff": 0.00003, "dev_mean_sr4_lnl_abs_diff": 0.000025, "reserve_mean_sr4_lnl_abs_diff": 0.000038, "overall_lnl_pearson_r": 1.0, "mean_compositional_bias_reduction_pct": 93.1259, "unrecoded_aa20_lba_failure_rate_pct": 100.0, "recoded_dayhoff6_lba_rescue_rate_pct": 100.0, "topology_and_lba_rejection_concordance_pct": 100.0, "total_native_ms": 9.2255, "total_iqtree_ms": 5820.2948, "speedup_factor": 630.8921, "cohorts": [ { "cohort_id": "DEV-01", "split": "Development", "name": "Asgard Archaea (Loki/Thor/Heimdall) + Eukaryota 2-Domain vs. 3-Domain LBA", "num_taxa": 8, "alignment_length_aa": 64, "variable_cols_aa20": 58, "variable_cols_dayhoff6": 16, "variable_cols_sr4": 16, "raw_aa_compositional_jsd_bits": 0.404072, "dayhoff6_compositional_jsd_bits": 0.038004, "compositional_bias_reduction_pct": 90.5947, "gen1_hardcoded_lnl_error": 148141.5762, "native_aa20_lnl": -783.0438, "iqtree_aa20_lnl": -783.0438, "abs_diff_aa20_lnl": 0.00001, "delta_lnl_true_minus_lba_aa20": -76.9101, "native_dayhoff6_lnl": -301.8976, "iqtree_dayhoff6_lnl": -301.8976, "abs_diff_dayhoff6_lnl": 9e-6, "native_sr4_lnl": -261.8651, "iqtree_sr4_lnl": -261.8651, "abs_diff_sr4_lnl": 0.00003, "native_dayhoff6_lba_trap_lnl": -406.8934, "iqtree_dayhoff6_lba_trap_lnl": -406.8934, "delta_lnl_true_minus_lba_dayhoff6": 104.9958, "mean_symbiont_metabolic_completeness_pct": 0.0, "mean_freeliving_metabolic_completeness_pct": 90.0, "regime_classification": "2-Domain Eocyte/Asgard+Eukaryota Sisterhood Recovered (Unrecoded AA-20 LBA Reversed)", "topology_and_gate_concordant": true, "native_runtime_ms": 0.9249, "iqtree_runtime_ms": 433.0792 }, { "cohort_id": "DEV-02", "split": "Development", "name": "Candidate Phyla Radiation (CPR / Patescibacteria) Monophyly & Auxotrophy", "num_taxa": 8, "alignment_length_aa": 64, "variable_cols_aa20": 58, "variable_cols_dayhoff6": 16, "variable_cols_sr4": 16, "raw_aa_compositional_jsd_bits": 0.404504, "dayhoff6_compositional_jsd_bits": 0.034029, "compositional_bias_reduction_pct": 91.5874, "gen1_hardcoded_lnl_error": 148196.5502, "native_aa20_lnl": -728.0698, "iqtree_aa20_lnl": -728.0698, "abs_diff_aa20_lnl": 0.000027, "delta_lnl_true_minus_lba_aa20": -70.0936, "native_dayhoff6_lnl": -280.2544, "iqtree_dayhoff6_lnl": -280.2544, "abs_diff_dayhoff6_lnl": 0.00004, "native_sr4_lnl": -244.0087, "iqtree_sr4_lnl": -244.0087, "abs_diff_sr4_lnl": 0.00002, "native_dayhoff6_lba_trap_lnl": -370.5838, "iqtree_dayhoff6_lba_trap_lnl": -370.5838, "delta_lnl_true_minus_lba_dayhoff6": 90.3294, "mean_symbiont_metabolic_completeness_pct": 26.6667, "mean_freeliving_metabolic_completeness_pct": 95.0, "regime_classification": "Monophyletic CPR Superphylum & Auxotrophic Symbiont Depletion (~26.7% Completeness)", "topology_and_gate_concordant": true, "native_runtime_ms": 0.9543, "iqtree_runtime_ms": 529.3582 }, { "cohort_id": "DEV-03", "split": "Development", "name": "DPANN Symbiotic Archaea (Nanoarchaeum/Parvarchaeota/Diapherotrites) Clade", "num_taxa": 8, "alignment_length_aa": 64, "variable_cols_aa20": 58, "variable_cols_dayhoff6": 16, "variable_cols_sr4": 16, "raw_aa_compositional_jsd_bits": 0.404504, "dayhoff6_compositional_jsd_bits": 0.034029, "compositional_bias_reduction_pct": 91.5874, "gen1_hardcoded_lnl_error": 148192.0082, "native_aa20_lnl": -732.6117, "iqtree_aa20_lnl": -732.6118, "abs_diff_aa20_lnl": 0.000055, "delta_lnl_true_minus_lba_aa20": -65.8834, "native_dayhoff6_lnl": -286.1882, "iqtree_dayhoff6_lnl": -286.1882, "abs_diff_dayhoff6_lnl": 0.000032, "native_sr4_lnl": -249.8424, "iqtree_sr4_lnl": -249.8424, "abs_diff_sr4_lnl": 0.000015, "native_dayhoff6_lba_trap_lnl": -374.1885, "iqtree_dayhoff6_lba_trap_lnl": -374.1885, "delta_lnl_true_minus_lba_dayhoff6": 88.0002, "mean_symbiont_metabolic_completeness_pct": 23.75, "mean_freeliving_metabolic_completeness_pct": 87.5, "regime_classification": "Monophyletic DPANN Symbiont Clade & Severe Biosynthetic Auxotrophy (~23.8% Completeness)", "topology_and_gate_concordant": true, "native_runtime_ms": 0.5142, "iqtree_runtime_ms": 454.2684 }, { "cohort_id": "DEV-04", "split": "Development", "name": "Hyperthermophilic Bacteria (Aquifex/Thermotoga) vs. Archaea IVYWREL Convergence", "num_taxa": 8, "alignment_length_aa": 64, "variable_cols_aa20": 58, "variable_cols_dayhoff6": 16, "variable_cols_sr4": 16, "raw_aa_compositional_jsd_bits": 0.425697, "dayhoff6_compositional_jsd_bits": 0.038307, "compositional_bias_reduction_pct": 91.0015, "gen1_hardcoded_lnl_error": 148174.4591, "native_aa20_lnl": -750.1609, "iqtree_aa20_lnl": -750.1609, "abs_diff_aa20_lnl": 0.000025, "delta_lnl_true_minus_lba_aa20": -51.4419, "native_dayhoff6_lnl": -277.5942, "iqtree_dayhoff6_lnl": -277.5942, "abs_diff_dayhoff6_lnl": 8e-6, "native_sr4_lnl": -241.853, "iqtree_sr4_lnl": -241.853, "abs_diff_sr4_lnl": 0.000026, "native_dayhoff6_lba_trap_lnl": -400.0725, "iqtree_dayhoff6_lba_trap_lnl": -400.0725, "delta_lnl_true_minus_lba_dayhoff6": 122.4783, "mean_symbiont_metabolic_completeness_pct": 0.0, "mean_freeliving_metabolic_completeness_pct": 90.625, "regime_classification": "Bacterial Monophyly Preserved Against Hyperthermophilic IVYWREL Convergence", "topology_and_gate_concordant": true, "native_runtime_ms": 0.8369, "iqtree_runtime_ms": 451.869 }, { "cohort_id": "DEV-05", "split": "Development", "name": "Alphaproteobacteria & Mitochondrial Origin vs. Outgroup AT-Rich LBA", "num_taxa": 8, "alignment_length_aa": 64, "variable_cols_aa20": 58, "variable_cols_dayhoff6": 16, "variable_cols_sr4": 16, "raw_aa_compositional_jsd_bits": 0.408195, "dayhoff6_compositional_jsd_bits": 0.032705, "compositional_bias_reduction_pct": 91.988, "gen1_hardcoded_lnl_error": 148176.7519, "native_aa20_lnl": -747.8681, "iqtree_aa20_lnl": -747.8681, "abs_diff_aa20_lnl": 0.000011, "delta_lnl_true_minus_lba_aa20": -73.8472, "native_dayhoff6_lnl": -280.3068, "iqtree_dayhoff6_lnl": -280.3068, "abs_diff_dayhoff6_lnl": 0.00002, "native_sr4_lnl": -244.4696, "iqtree_sr4_lnl": -244.4697, "abs_diff_sr4_lnl": 0.000054, "native_dayhoff6_lba_trap_lnl": -380.6261, "iqtree_dayhoff6_lba_trap_lnl": -380.6261, "delta_lnl_true_minus_lba_dayhoff6": 100.3193, "mean_symbiont_metabolic_completeness_pct": 29.4444, "mean_freeliving_metabolic_completeness_pct": 93.0, "regime_classification": "Mitochondrial-Rickettsiales Sisterhood Resolved (AT-Rich LBA Reversed)", "topology_and_gate_concordant": true, "native_runtime_ms": 0.9973, "iqtree_runtime_ms": 508.0633 }, { "cohort_id": "DEV-06", "split": "Development", "name": "Symmetrically Permuted Within-Class Compositional Control (0-Beaker Gate)", "num_taxa": 8, "alignment_length_aa": 64, "variable_cols_aa20": 56, "variable_cols_dayhoff6": 1, "variable_cols_sr4": 1, "raw_aa_compositional_jsd_bits": 0.498986, "dayhoff6_compositional_jsd_bits": 0.000128, "compositional_bias_reduction_pct": 99.9743, "gen1_hardcoded_lnl_error": 147572.0039, "native_aa20_lnl": -1352.616, "iqtree_aa20_lnl": -1352.6161, "abs_diff_aa20_lnl": 0.000076, "delta_lnl_true_minus_lba_aa20": 0.0, "native_dayhoff6_lnl": -249.9731, "iqtree_dayhoff6_lnl": -249.9731, "abs_diff_dayhoff6_lnl": 0.000029, "native_sr4_lnl": -221.7693, "iqtree_sr4_lnl": -221.7693, "abs_diff_sr4_lnl": 4e-6, "native_dayhoff6_lba_trap_lnl": -249.9731, "iqtree_dayhoff6_lba_trap_lnl": -249.9731, "delta_lnl_true_minus_lba_dayhoff6": 0.0, "mean_symbiont_metabolic_completeness_pct": 0.0, "mean_freeliving_metabolic_completeness_pct": 96.6667, "regime_classification": "0-Beaker Negative Control Rejected (ΔlnL = 0.0000 Under Recoding; Pure Within-Class Drift)", "topology_and_gate_concordant": true, "native_runtime_ms": 0.8332, "iqtree_runtime_ms": 500.3208 }, { "cohort_id": "RES-01", "split": "Reserve", "name": "Primary Plastid Endosymbiosis (Gloeomargarita + Chloroplast RP16 vs. Melainabacteria)", "num_taxa": 8, "alignment_length_aa": 64, "variable_cols_aa20": 58, "variable_cols_dayhoff6": 16, "variable_cols_sr4": 16, "raw_aa_compositional_jsd_bits": 0.408195, "dayhoff6_compositional_jsd_bits": 0.032705, "compositional_bias_reduction_pct": 91.988, "gen1_hardcoded_lnl_error": 148176.1898, "native_aa20_lnl": -748.4302, "iqtree_aa20_lnl": -748.4302, "abs_diff_aa20_lnl": 2e-6, "delta_lnl_true_minus_lba_aa20": -73.2437, "native_dayhoff6_lnl": -281.1993, "iqtree_dayhoff6_lnl": -281.1993, "abs_diff_dayhoff6_lnl": 0.000026, "native_sr4_lnl": -245.2155, "iqtree_sr4_lnl": -245.2155, "abs_diff_sr4_lnl": 0.000046, "native_dayhoff6_lba_trap_lnl": -381.4718, "iqtree_dayhoff6_lba_trap_lnl": -381.4718, "delta_lnl_true_minus_lba_dayhoff6": 100.2724, "mean_symbiont_metabolic_completeness_pct": 30.8333, "mean_freeliving_metabolic_completeness_pct": 92.5, "regime_classification": "Gloeomargarita-Archaeplastida Plastid Sisterhood Confirmed (AT-Rich LBA Rejected)", "topology_and_gate_concordant": true, "native_runtime_ms": 0.9074, "iqtree_runtime_ms": 485.2219 }, { "cohort_id": "RES-02", "split": "Reserve", "name": "Microsporidia (Encephalitozoon/Nosema) Fungal Placement vs. Basal Archezoa LBA", "num_taxa": 9, "alignment_length_aa": 64, "variable_cols_aa20": 58, "variable_cols_dayhoff6": 16, "variable_cols_sr4": 16, "raw_aa_compositional_jsd_bits": 0.392365, "dayhoff6_compositional_jsd_bits": 0.030192, "compositional_bias_reduction_pct": 92.3052, "gen1_hardcoded_lnl_error": 148165.0615, "native_aa20_lnl": -759.5584, "iqtree_aa20_lnl": -759.5585, "abs_diff_aa20_lnl": 0.000051, "delta_lnl_true_minus_lba_aa20": -68.0171, "native_dayhoff6_lnl": -314.2564, "iqtree_dayhoff6_lnl": -314.2564, "abs_diff_dayhoff6_lnl": 0.000024, "native_sr4_lnl": -277.4971, "iqtree_sr4_lnl": -277.4972, "abs_diff_sr4_lnl": 0.000053, "native_dayhoff6_lba_trap_lnl": -402.7208, "iqtree_dayhoff6_lba_trap_lnl": -402.7208, "delta_lnl_true_minus_lba_dayhoff6": 88.4644, "mean_symbiont_metabolic_completeness_pct": 33.6667, "mean_freeliving_metabolic_completeness_pct": 93.3333, "regime_classification": "Holomycota Fungal Sisterhood of Microsporidia Recovered (Archezoa LBA Rejected)", "topology_and_gate_concordant": true, "native_runtime_ms": 0.9061, "iqtree_runtime_ms": 492.7366 }, { "cohort_id": "RES-03", "split": "Reserve", "name": "Insect Endosymbiont Gammaproteobacteria (Buchnera/Wigglesworthia) vs. AT-Rich Outgroup", "num_taxa": 9, "alignment_length_aa": 64, "variable_cols_aa20": 58, "variable_cols_dayhoff6": 16, "variable_cols_sr4": 16, "raw_aa_compositional_jsd_bits": 0.392365, "dayhoff6_compositional_jsd_bits": 0.030192, "compositional_bias_reduction_pct": 92.3052, "gen1_hardcoded_lnl_error": 147999.0474, "native_aa20_lnl": -925.5726, "iqtree_aa20_lnl": -925.5726, "abs_diff_aa20_lnl": 0.000019, "delta_lnl_true_minus_lba_aa20": -244.9884, "native_dayhoff6_lnl": -302.024, "iqtree_dayhoff6_lnl": -302.024, "abs_diff_dayhoff6_lnl": 0.000028, "native_sr4_lnl": -265.6413, "iqtree_sr4_lnl": -265.6412, "abs_diff_sr4_lnl": 0.000051, "native_dayhoff6_lba_trap_lnl": -392.3796, "iqtree_dayhoff6_lba_trap_lnl": -392.3796, "delta_lnl_true_minus_lba_dayhoff6": 90.3556, "mean_symbiont_metabolic_completeness_pct": 29.0, "mean_freeliving_metabolic_completeness_pct": 97.0833, "regime_classification": "Enterobacterales Placement of Insect Endosymbionts Confirmed (Tenericutes LBA Rejected)", "topology_and_gate_concordant": true, "native_runtime_ms": 0.5932, "iqtree_runtime_ms": 531.5337 }, { "cohort_id": "RES-04", "split": "Reserve", "name": "Non-Bilaterian Metazoan Base (Porifera/Ctenophora/Cnidaria) vs. Choanoflagellate LBA", "num_taxa": 8, "alignment_length_aa": 64, "variable_cols_aa20": 58, "variable_cols_dayhoff6": 16, "variable_cols_sr4": 16, "raw_aa_compositional_jsd_bits": 0.404504, "dayhoff6_compositional_jsd_bits": 0.034029, "compositional_bias_reduction_pct": 91.5874, "gen1_hardcoded_lnl_error": 148194.0007, "native_aa20_lnl": -730.6192, "iqtree_aa20_lnl": -730.6193, "abs_diff_aa20_lnl": 0.000054, "delta_lnl_true_minus_lba_aa20": -65.7936, "native_dayhoff6_lnl": -285.4413, "iqtree_dayhoff6_lnl": -285.4413, "abs_diff_dayhoff6_lnl": 0.00003, "native_sr4_lnl": -249.0513, "iqtree_sr4_lnl": -249.0513, "abs_diff_sr4_lnl": 0.00003, "native_dayhoff6_lba_trap_lnl": -372.402, "iqtree_dayhoff6_lba_trap_lnl": -372.402, "delta_lnl_true_minus_lba_dayhoff6": 86.9607, "mean_symbiont_metabolic_completeness_pct": 0.0, "mean_freeliving_metabolic_completeness_pct": 91.875, "regime_classification": "Monophyletic Crown Metazoa Resolved Against Choanoflagellate Outgroup LBA", "topology_and_gate_concordant": true, "native_runtime_ms": 0.7176, "iqtree_runtime_ms": 457.799 }, { "cohort_id": "RES-05", "split": "Reserve", "name": "TACK Archaeal Superphylum (Thaumarchaeota/Aigarchaeota/Crenarchaeota/Korarchaeota)", "num_taxa": 8, "alignment_length_aa": 64, "variable_cols_aa20": 58, "variable_cols_dayhoff6": 16, "variable_cols_sr4": 16, "raw_aa_compositional_jsd_bits": 0.389172, "dayhoff6_compositional_jsd_bits": 0.02873, "compositional_bias_reduction_pct": 92.6177, "gen1_hardcoded_lnl_error": 148192.7785, "native_aa20_lnl": -731.8415, "iqtree_aa20_lnl": -731.8415, "abs_diff_aa20_lnl": 0.000025, "delta_lnl_true_minus_lba_aa20": -104.7319, "native_dayhoff6_lnl": -273.1783, "iqtree_dayhoff6_lnl": -273.1783, "abs_diff_dayhoff6_lnl": 0.000045, "native_sr4_lnl": -237.6145, "iqtree_sr4_lnl": -237.6145, "abs_diff_sr4_lnl": 0.00001, "native_dayhoff6_lba_trap_lnl": -345.9598, "iqtree_dayhoff6_lba_trap_lnl": -345.9598, "delta_lnl_true_minus_lba_dayhoff6": 72.7814, "mean_symbiont_metabolic_completeness_pct": 48.3333, "mean_freeliving_metabolic_completeness_pct": 85.2381, "regime_classification": "Monophyletic TACK Superphylum Confirmed Across Mesophile-Thermophile Transition", "topology_and_gate_concordant": true, "native_runtime_ms": 0.4982, "iqtree_runtime_ms": 484.6357 }, { "cohort_id": "RES-06", "split": "Reserve", "name": "Untouched Reserve Symmetrically Permuted Decoy Control (0-Beaker Gate)", "num_taxa": 8, "alignment_length_aa": 64, "variable_cols_aa20": 56, "variable_cols_dayhoff6": 1, "variable_cols_sr4": 1, "raw_aa_compositional_jsd_bits": 0.498986, "dayhoff6_compositional_jsd_bits": 0.000128, "compositional_bias_reduction_pct": 99.9743, "gen1_hardcoded_lnl_error": 147535.1892, "native_aa20_lnl": -1389.4308, "iqtree_aa20_lnl": -1389.4308, "abs_diff_aa20_lnl": 0.00001, "delta_lnl_true_minus_lba_aa20": 0.0, "native_dayhoff6_lnl": -234.0195, "iqtree_dayhoff6_lnl": -234.0195, "abs_diff_dayhoff6_lnl": 0.000027, "native_sr4_lnl": -206.1329, "iqtree_sr4_lnl": -206.1329, "abs_diff_sr4_lnl": 0.00004, "native_dayhoff6_lba_trap_lnl": -234.0195, "iqtree_dayhoff6_lba_trap_lnl": -234.0195, "delta_lnl_true_minus_lba_dayhoff6": 0.0, "mean_symbiont_metabolic_completeness_pct": 0.0, "mean_freeliving_metabolic_completeness_pct": 95.0, "regime_classification": "0-Beaker Reserve Negative Control Rejected (ΔlnL = 0.0000 Under Recoding)", "topology_and_gate_concordant": true, "native_runtime_ms": 0.5422, "iqtree_runtime_ms": 491.409 } ], "ascii_summary_table": "======================================================================================================================================================\n TOOL BENCHMARK #19: Native Rust RP16 Supermatrix & Dayhoff-6/SR4 Recoder vs. Live IQ-TREE v2.4.0 (-st AA POISSON+FQ & -st MORPH MK)\n======================================================================================================================================================\nCohort Split Nat AA20 IQ AA20 Nat Day6 IQ Day6 Nat SR4 IQ SR4 dLnL_AA20 dLnL_Day6 BiasRed% Concordant\n------------------------------------------------------------------------------------------------------------------------------------------------------\nDEV-01 Development -783.0438 -783.0438 -301.8976 -301.8976 -261.8651 -261.8651 -76.9101 +104.9958 90.59% YES (100%)\nDEV-02 Development -728.0698 -728.0698 -280.2544 -280.2544 -244.0087 -244.0087 -70.0936 +90.3294 91.59% YES (100%)\nDEV-03 Development -732.6117 -732.6118 -286.1882 -286.1882 -249.8424 -249.8424 -65.8834 +88.0002 91.59% YES (100%)\nDEV-04 Development -750.1609 -750.1609 -277.5942 -277.5942 -241.8530 -241.8530 -51.4419 +122.4783 91.00% YES (100%)\nDEV-05 Development -747.8681 -747.8681 -280.3068 -280.3068 -244.4696 -244.4697 -73.8472 +100.3193 91.99% YES (100%)\nDEV-06 Development -1352.6160 -1352.6161 -249.9731 -249.9731 -221.7693 -221.7693 +0.0000 +0.0000 99.97% YES (100%)\nRES-01 Reserve -748.4302 -748.4302 -281.1993 -281.1993 -245.2155 -245.2155 -73.2437 +100.2724 91.99% YES (100%)\nRES-02 Reserve -759.5584 -759.5585 -314.2564 -314.2564 -277.4971 -277.4972 -68.0171 +88.4644 92.31% YES (100%)\nRES-03 Reserve -925.5726 -925.5726 -302.0240 -302.0240 -265.6413 -265.6412 -244.9884 +90.3556 92.31% YES (100%)\nRES-04 Reserve -730.6192 -730.6193 -285.4413 -285.4413 -249.0513 -249.0513 -65.7936 +86.9607 91.59% YES (100%)\nRES-05 Reserve -731.8415 -731.8415 -273.1783 -273.1783 -237.6145 -237.6145 -104.7319 +72.7814 92.62% YES (100%)\nRES-06 Reserve -1389.4308 -1389.4308 -234.0195 -234.0195 -206.1329 -206.1329 +0.0000 +0.0000 99.97% YES (100%)\n------------------------------------------------------------------------------------------------------------------------------------------------------\nSUMMARY: Dev |dLnL_D6|=0.0000, Res |dLnL_D6|=0.0000 | Dev |dLnL_SR4|=0.0000, Res |dLnL_SR4|=0.0000 | Pearson r=1.000000 | Speedup=630.9x\n" }