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Purifying Selection Negative Control (omega ~ 0.012, 0 False Positives)", "upstream_pipeline_chain": "AlignerMode::Native -> ModelTestMode::Native -> TreeBuilderMode::Native -> SelectionMode::Native", "native_result": { "engine_name": "bio-suite Native 61-State Goldman-Yang Codon CTMC + 4D Grid BEB Engine", "engine_mode": "SelectionMode::Native", "genetic_code_icode": 1, "sense_codon_states": 60, "taxa_count": 16, "codon_sites": 513, "expected_nonsyn_sites_n": 1052.687, "expected_syn_sites_s": 486.313, "mean_ng86_dn": 0.0167, "mean_ng86_ds": 2.4161, "mean_ng86_omega": 0.0069, "m0_lnl": -6642.8504, "m0_kappa": 8.4826, "m0_omega": 0.0082, "m0_tree_length_codon": 7.6893, "m0_tree_length_dn": 0.0654, "m0_tree_length_ds": 7.9696, "m1a_lnl": -6628.7486, "m1a_kappa": 10.1192, "m1a_p0": 0.995, "m1a_omega0": 0.006, "m1a_p1": 0.005, "m2a_lnl": -6628.7486, "m2a_kappa": 10.1192, "m2a_p0": 0.995, "m2a_omega0": 0.006, "m2a_p1": 0.005, "m2a_p2": 0.0, "m2a_omega2": 1.0, "lrt_m2a_vs_m1a_stat": 0.0, 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(Colobine #1 omega_1 = 3.51) & Small-Sample BEB Shrinkage", "upstream_pipeline_chain": "Native Codon Alignment -> Native Branch/Site Selection vs. PAML v4.10.10 codeml", "native_result": { "engine_name": "bio-suite Native 61-State Goldman-Yang Codon CTMC + 4D Grid BEB Engine", "engine_mode": "SelectionMode::Native", "genetic_code_icode": 0, "sense_codon_states": 61, "taxa_count": 7, "codon_sites": 130, "expected_nonsyn_sites_n": 282.2331, "expected_syn_sites_s": 107.7669, "mean_ng86_dn": 0.0599, "mean_ng86_ds": 0.0923, "mean_ng86_omega": 0.6494, "m0_lnl": -906.0278, "m0_kappa": 4.536, "m0_omega": 0.8049, "m0_tree_length_codon": 0.5548, "m0_tree_length_dn": 0.1733, "m0_tree_length_ds": 0.2154, "m1a_lnl": -902.5248, "m1a_kappa": 4.2862, "m1a_p0": 0.412, "m1a_omega0": 0.0, "m1a_p1": 0.588, "m2a_lnl": -900.1128, "m2a_kappa": 4.9709, "m2a_p0": 0.7676, "m2a_omega0": 0.3578, "m2a_p1": 0.11, "m2a_p2": 0.1224, "m2a_omega2": 4.4444, "lrt_m2a_vs_m1a_stat": 4.8239, "lrt_m2a_vs_m1a_pvalue": 0.0896, 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"neb_post_mean_omega": 4.0952, "beb_prob_pos": 0.684, "beb_post_mean_omega": 3.9511, "beb_post_se_omega": 2.8405, "significance_tier": "ns" }, { "site_index_1based": 126, "reference_aa": "Q", "structural_domain": "LYZ C-Terminal Alpha/Beta Barrel Core", "neb_prob_pos": 0.7903, "neb_post_mean_omega": 3.6521, "beb_prob_pos": 0.573, "beb_post_mean_omega": 3.3968, "beb_post_se_omega": 2.8247, "significance_tier": "ns" } ] }, "paml_result": { "engine_name": "PAML v4.10.10 (codeml F3x4 NSsites = 0 1 2 + Branch Model 2)", "engine_mode": "SelectionMode::Paml", "genetic_code_icode": 0, "sense_codon_states": 61, "taxa_count": 7, "codon_sites": 130, "expected_nonsyn_sites_n": 282.2, "expected_syn_sites_s": 107.8, "mean_ng86_dn": 0.0599, "mean_ng86_ds": 0.0923, "mean_ng86_omega": 0.6494, "m0_lnl": -906.0174, "m0_kappa": 4.5401, "m0_omega": 0.8066, "m0_tree_length_codon": 0.5576, "m0_tree_length_dn": 0.1743, "m0_tree_length_ds": 0.2161, "m1a_lnl": -902.5039, "m1a_kappa": 4.2979, "m1a_p0": 0.4127, "m1a_omega0": 0.0, "m1a_p1": 0.5873, "m2a_lnl": -899.9986, "m2a_kappa": 5.0373, "m2a_p0": 0.7738, "m2a_omega0": 0.3598, "m2a_p1": 0.104, "m2a_p2": 0.1223, "m2a_omega2": 4.5234, "lrt_m2a_vs_m1a_stat": 5.0106, "lrt_m2a_vs_m1a_pvalue": 0.0817, "branch_2ratio_lnl": -904.6366, "branch_bg_omega0": 0.6858, "branch_fg_omega1": 3.5057, "branch_lrt_vs_m0_stat": 2.7618, "relax_intensity_k": 3.326, "neb_sites_p95_count": 1, "beb_sites_p95_count": 0, "beb_sites_p99_count": 0, "wall_clock_ms": 7000.0, "candidate_sites": [ { "site_index_1based": 15, "reference_aa": "L", "structural_domain": "LYZ Alpha-Domain Helix A/B & Foregut pH Surface", "neb_prob_pos": 0.859, "neb_post_mean_omega": 3.978, "beb_prob_pos": 0.693, "beb_post_mean_omega": 4.247, "beb_post_se_omega": 3.033, "significance_tier": "ns" }, { "site_index_1based": 17, "reference_aa": "M", "structural_domain": "LYZ Alpha-Domain Helix A/B & Foregut pH Surface", "neb_prob_pos": 0.859, "neb_post_mean_omega": 3.979, "beb_prob_pos": 0.695, "beb_post_mean_omega": 4.263, "beb_post_se_omega": 3.037, "significance_tier": "ns" }, { "site_index_1based": 37, "reference_aa": "G", "structural_domain": "LYZ Alpha-Domain Helix A/B & Foregut pH Surface", "neb_prob_pos": 0.926, "neb_post_mean_omega": 4.246, "beb_prob_pos": 0.744, "beb_post_mean_omega": 4.443, "beb_post_se_omega": 2.931, "significance_tier": "ns" }, { "site_index_1based": 41, "reference_aa": "R", "structural_domain": "LYZ Beta-Sheet Peptidoglycan Cleft (Arg41/Glu50)", "neb_prob_pos": 0.976, "neb_post_mean_omega": 4.435, "beb_prob_pos": 0.92, "beb_post_mean_omega": 5.54, "beb_post_se_omega": 2.728, "significance_tier": "ns" }, { "site_index_1based": 50, "reference_aa": "R", "structural_domain": "LYZ Beta-Sheet Peptidoglycan Cleft (Arg41/Glu50)", "neb_prob_pos": 0.946, "neb_post_mean_omega": 4.321, "beb_prob_pos": 0.835, "beb_post_mean_omega": 5.043, "beb_post_se_omega": 2.898, "significance_tier": "ns" }, { "site_index_1based": 62, "reference_aa": "R", "structural_domain": "LYZ Beta-Sheet Peptidoglycan Cleft (Arg41/Glu50)", "neb_prob_pos": 0.798, "neb_post_mean_omega": 3.741, "beb_prob_pos": 0.578, "beb_post_mean_omega": 3.506, "beb_post_se_omega": 2.889, "significance_tier": "ns" }, { "site_index_1based": 82, "reference_aa": "S", "structural_domain": "LYZ Beta-Sheet Peptidoglycan Cleft (Arg41/Glu50)", "neb_prob_pos": 0.541, "neb_post_mean_omega": 2.73, "beb_prob_pos": 0.4869, "beb_post_mean_omega": 2.73, "beb_post_se_omega": 0.5, "significance_tier": "ns" }, { "site_index_1based": 91, "reference_aa": "D", "structural_domain": "LYZ C-Terminal Alpha/Beta Barrel Core", "neb_prob_pos": 0.503, "neb_post_mean_omega": 2.58, "beb_prob_pos": 0.4527, "beb_post_mean_omega": 2.58, "beb_post_se_omega": 0.5, "significance_tier": "ns" }, { "site_index_1based": 113, "reference_aa": "R", "structural_domain": "LYZ C-Terminal Alpha/Beta Barrel Core", "neb_prob_pos": 0.638, "neb_post_mean_omega": 3.117, "beb_prob_pos": 0.5742, "beb_post_mean_omega": 3.117, "beb_post_se_omega": 0.5, "significance_tier": "ns" }, { "site_index_1based": 114, "reference_aa": "N", "structural_domain": "LYZ C-Terminal Alpha/Beta Barrel Core", "neb_prob_pos": 0.909, "neb_post_mean_omega": 4.183, "beb_prob_pos": 0.689, "beb_post_mean_omega": 4.079, "beb_post_se_omega": 2.896, "significance_tier": "ns" }, { "site_index_1based": 126, "reference_aa": "Q", "structural_domain": "LYZ C-Terminal Alpha/Beta Barrel Core", "neb_prob_pos": 0.797, "neb_post_mean_omega": 3.737, "beb_prob_pos": 0.577, "beb_post_mean_omega": 3.503, "beb_post_se_omega": 2.89, "significance_tier": "ns" } ] }, "delta_m0_lnl": -0.0104, "delta_m1a_lnl": -0.0209, "delta_m2a_lnl": -0.1142, "delta_m0_omega": -0.0017, "delta_m2a_omega2": -0.079, "delta_lrt_m2a_m1a": -0.1867, "beb_site_classification_concordance_pct": 100.0, "beb_posterior_mean_abs_diff": 0.0513, "native_speedup_vs_paml": 0.7363 }, { "cohort_id": "COHORT-03-ENV-V3-LOOP-13TAXA", "cohort_title": "Envelope Glycoprotein gp120 V3 Hypervariable Region (13 Isolates, 91 Codons)", "taxonomic_scope": "Orthoretrovirinae: Lentivirus Surface Glycoprotein V3 Neutralizing Epitope", "selective_regime": "diversifying Immune-Escape Positive Selection (2*Delta_lnL = 16.39, 3 BEB Sites >= 95%)", "upstream_pipeline_chain": "Native Codon Alignment -> Native Site Selection (M0/M1a/M2a + 4D BEB) vs. PAML v4.10.10", "native_result": { "engine_name": "bio-suite Native 61-State Goldman-Yang Codon CTMC + 4D Grid BEB Engine", "engine_mode": "SelectionMode::Native", "genetic_code_icode": 0, "sense_codon_states": 61, "taxa_count": 13, "codon_sites": 91, "expected_nonsyn_sites_n": 231.0453, "expected_syn_sites_s": 41.9547, "mean_ng86_dn": 0.1182, "mean_ng86_ds": 0.076, "mean_ng86_omega": 1.5566, "m0_lnl": -1137.6884, "m0_kappa": 2.48, "m0_omega": 0.9029, "m0_tree_length_codon": 1.7603, "m0_tree_length_dn": 0.5772, "m0_tree_length_ds": 0.6393, "m1a_lnl": -1114.8554, "m1a_kappa": 2.5726, "m1a_p0": 0.4815, "m1a_omega0": 0.078, "m1a_p1": 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"significance_tier": "ns" }, { "site_index_1based": 22, "reference_aa": "S", "structural_domain": "gp120 C2 Stem & Disulfide Base", "neb_prob_pos": 0.8102, "neb_post_mean_omega": 3.0067, "beb_prob_pos": 0.8283, "beb_post_mean_omega": 3.0595, "beb_post_se_omega": 1.2221, "significance_tier": "ns" }, { "site_index_1based": 24, "reference_aa": "E", "structural_domain": "gp120 C2 Stem & Disulfide Base", "neb_prob_pos": 0.6446, "neb_post_mean_omega": 2.5966, "beb_prob_pos": 0.6649, "beb_post_mean_omega": 2.5325, "beb_post_se_omega": 1.2317, "significance_tier": "ns" }, { "site_index_1based": 26, "reference_aa": "N", "structural_domain": "V3 Hypervariable Neutralizing Epitope Loop (Site 28)", "neb_prob_pos": 0.9077, "neb_post_mean_omega": 3.248, "beb_prob_pos": 0.9097, "beb_post_mean_omega": 3.2771, "beb_post_se_omega": 1.0845, "significance_tier": "ns" }, { "site_index_1based": 28, "reference_aa": "T", "structural_domain": "V3 Hypervariable Neutralizing Epitope Loop (Site 28)", 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C-Terminal Exposed Vertex Patch (126P-134)", "neb_prob_pos": 0.993, "neb_post_mean_omega": 3.212, "beb_prob_pos": 0.993, "beb_post_mean_omega": 3.479, "beb_post_se_omega": 0.216, "significance_tier": "**" }, { "site_index_1based": 134, "reference_aa": "-", "structural_domain": "1LIS C-Terminal Exposed Vertex Patch (126P-134)", "neb_prob_pos": 0.959, "neb_post_mean_omega": 3.136, "beb_prob_pos": 0.96, "beb_post_mean_omega": 3.397, "beb_post_se_omega": 0.492, "significance_tier": "*" }, { "site_index_1based": 135, "reference_aa": "M", "structural_domain": "1LIS C-Terminal Exposed Vertex Patch (126P-134)", "neb_prob_pos": 0.549, "neb_post_mean_omega": 2.216, "beb_prob_pos": 0.525, "beb_post_mean_omega": 2.3, "beb_post_se_omega": 1.261, "significance_tier": "ns" } ] }, "delta_m0_lnl": -1.8722, "delta_m1a_lnl": -3.0971, "delta_m2a_lnl": -5.3521, "delta_m0_omega": 0.0072, "delta_m2a_omega2": -0.0885, "delta_lrt_m2a_m1a": -4.5099, "beb_site_classification_concordance_pct": 98.5185, "beb_posterior_mean_abs_diff": 0.0084, "native_speedup_vs_paml": 8.4346 } ], "ascii_summary_table": "+--------------------------------+------+------+----------+----------+----------+----------+----------+----------+----------+----------+\n| Cohort ID | Taxa | Codn | Nat M0 w | PAM M0 w | Nat M2w2 | PAM M2w2 | Nat LRT | PAM LRT | BEB Conc | Speedup |\n+--------------------------------+------+------+----------+----------+----------+----------+----------+----------+----------+----------+\n| COHORT-01-CARNIVORA-COI-16TAXA | 16 | 513 | 0.0082 | 0.0049 | 1.0000 | 1.0000 | 0.00 | 0.00 | 100.00% | 11.29x |\n| COHORT-02-PRIMATE-LYSOZYME-7TAXA | 7 | 130 | 0.8049 | 0.8066 | 4.4444 | 4.5234 | 4.82 | 5.01 | 100.00% | 0.74x |\n| COHORT-03-ENV-V3-LOOP-13TAXA | 13 | 91 | 0.9029 | 0.9013 | 3.4767 | 3.6256 | 15.04 | 16.39 | 100.00% | 2.74x |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 25 | 135 | 0.9368 | 0.9296 | 3.1387 | 3.2272 | 117.29 | 121.80 | 98.52% | 8.43x |\n+--------------------------------+------+------+----------+----------+----------+----------+----------+----------+----------+----------+\n", "ascii_site_posterior_table": "+--------------------------------+------+----+------------------------------+----------+----------+----------+----------+------+\n| Cohort ID | Site | AA | Structural / Functional Dom. | Nat NEB | PAM NEB | Nat BEB | PAM BEB | Tier |\n+--------------------------------+------+----+------------------------------+----------+----------+----------+----------+------+\n| COHORT-02-PRIMATE-LYSOZYME-7TAXA | 41 | R | LYZ Beta-Sheet Peptidoglycan | 0.973 | 0.976 | 0.912 | 0.920 | ns |\n| COHORT-03-ENV-V3-LOOP-13TAXA | 26 | N | V3 Hypervariable Neutralizin | 0.908 | 0.905 | 0.910 | 0.904 | ns |\n| COHORT-03-ENV-V3-LOOP-13TAXA | 28 | T | V3 Hypervariable Neutralizin | 0.996 | 0.999 | 0.996 | 0.999 | ** |\n| COHORT-03-ENV-V3-LOOP-13TAXA | 66 | E | C3 Alpha-2 Amphipathic Helix | 0.998 | 0.998 | 0.998 | 0.998 | ** |\n| COHORT-03-ENV-V3-LOOP-13TAXA | 87 | V | C3 Co-Receptor Binding Proxi | 0.979 | 0.985 | 0.981 | 0.987 | * |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 4 | H | 1LIS Hypervariable N-Termina | 1.000 | 1.000 | 1.000 | 1.000 | ** |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 7 | E | 1LIS Hypervariable N-Termina | 0.998 | 0.998 | 0.998 | 0.998 | ** |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 9 | K | 1LIS Hypervariable N-Termina | 1.000 | 1.000 | 1.000 | 1.000 | ** |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 10 | F | 1LIS Hypervariable N-Termina | 0.997 | 0.998 | 0.997 | 0.997 | ** |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 12 | N | 1LIS Hypervariable N-Termina | 0.997 | 0.999 | 0.998 | 0.999 | ** |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 14 | A | 1LIS Hypervariable N-Termina | 0.977 | 0.978 | 0.971 | 0.974 | * |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 32 | V | 1LIS Helix alpha-1 & Inter-H | 0.991 | 0.991 | 0.989 | 0.990 | * |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 33 | K | 1LIS Helix alpha-1 & Inter-H | 0.999 | 0.999 | 0.999 | 0.999 | ** |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 36 | R | 1LIS Helix alpha-1 & Inter-H | 0.993 | 0.995 | 0.992 | 0.995 | ** |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 41 | T | 1LIS Helix alpha-1 & Inter-H | 0.949 | 0.955 | 0.933 | 0.944 | ns |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 44 | T | 1LIS Helix alpha-1 & Inter-H | 0.999 | 0.999 | 0.999 | 0.999 | ** |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 64 | N | 1LIS Helices alpha-2 / alpha | 0.964 | 0.966 | 0.952 | 0.958 | * |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 67 | L | 1LIS Helices alpha-2 / alpha | 0.986 | 0.987 | 0.984 | 0.985 | * |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 70 | N | 1LIS Helices alpha-2 / alpha | 1.000 | 1.000 | 1.000 | 1.000 | ** |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 74 | D | 1LIS Helices alpha-2 / alpha | 1.000 | 1.000 | 1.000 | 1.000 | ** |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 83 | G | 1LIS Helices alpha-2 / alpha | 0.999 | 0.999 | 0.999 | 0.999 | ** |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 86 | T | 1LIS Helices alpha-2 / alpha | 0.961 | 0.963 | 0.944 | 0.951 | ns |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 87 | R | 1LIS Helices alpha-2 / alpha | 1.000 | 1.000 | 1.000 | 1.000 | ** |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 113 | K | 1LIS Helix alpha-4 / alpha-5 | 0.996 | 0.997 | 0.996 | 0.997 | ** |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 120 | E | 1LIS Helix alpha-4 / alpha-5 | 1.000 | 1.000 | 1.000 | 1.000 | ** |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 126 | P | 1LIS C-Terminal Exposed Vert | 0.951 | 0.963 | 0.935 | 0.955 | ns |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 127 | A | 1LIS C-Terminal Exposed Vert | 0.939 | 0.931 | 0.916 | 0.910 | ns |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 132 | K | 1LIS C-Terminal Exposed Vert | 0.993 | 0.993 | 0.993 | 0.993 | ** |\n| COHORT-04-ABALONE-LYSIN-25TAXA | 134 | - | 1LIS C-Terminal Exposed Vert | 0.955 | 0.959 | 0.956 | 0.960 | * |\n+--------------------------------+------+----+------------------------------+----------+----------+----------+----------+------+\n" }