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"mean_branch_support_pct": 99.9998, "newick_tree": "(Staphylococcus_aureus:0.49836,(Bacillus_subtilis:0.00016,Pseudomonas_aeruginosa:6.18242)100:0.49836);" }, "ascii_cohort_table": "+--------------------------------------------------------------------------------------------------+\n| COHORT-01-PROK-ORIC-PARALOGS — Bacterial oriC Synteny (dnaA-dnaN-recF-gyrB-gyrA) + GyrB2 In-Paralog & ParC Out-Paralog |\n+------------------------------+----------------------+----------------------+---------------------+\n| Metric | Native SW-BLOSUM62 | DIAMOND v2.2.8 SWIPE | DIAMOND v2.2.8 Fast |\n+------------------------------+----------------------+----------------------+---------------------+\n| Proteins / Species | 16 / 3 | 16 / 3 | 16 / 3 |\n| Cross-Species Hits | 32 | 32 | 24 |\n| Twilight Hits (<35% ID) | 8 | 8 | 0 |\n| 1:1 RBH Ortholog Pairs | 13 | 13 | 9 |\n| Co-Ortholog In-Paralog Pairs | 1 | 1 | 1 |\n| Out-Paralog Pairs Rejected | 4 | 4 | 3 |\n| Single-Copy Core Orthogroups | 3 | 3 | 1 |\n| Length Slope b (Raw -> Norm) | 0.6066 -> 0.0000 | 0.6077 -> 0.0000 | 0.1000 -> 0.0228 |\n| Wall-Clock Runtime (ms) | 302.36 | 129.62 | 246.92 |\n+------------------------------+----------------------+----------------------+---------------------+" }, { "cohort_id": "COHORT-02-ENTERIC-SYNTENY-10LOCI", "cohort_title": "Enterobacterial thrLABC-dnaKJ-ileS 10-Gene Synteny & +31.4 kb Genomic Island Shift", "taxonomic_scope": "Prokaryota (Enterobacteriaceae: Escherichia coli K-12 MG1655 vs. Salmonella enterica LT2)", "biological_focus": "1:1 Core Orthology Recovery Across a +31.4 kb Horizontal Island Insertion (NhaA-RibF-IleS Shift)", "protein_count": 20, "species_count": 2, "native_result": { "engine_name": "bio-suite Native 4-Stage SW-BLOSUM62 + Length-Normalized RBH Engine", "engine_mode": "Native", "protein_count": 20, "species_count": 2, "total_all_vs_all_hits": 40, "cross_species_hits": 20, "twilight_zone_hits_under_35pct": 0, "rbh_ortholog_pairs_count": 10, "in_paralog_pairs_count": 0, "out_paralog_pairs_rejected": 0, "inferred_orthogroups_count": 10, "single_copy_core_orthogroups": 10, "length_bias_slope_raw_b": 0.4923, "length_bias_slope_normalized_b": 0.0, "wall_clock_ms": 387.211, "orthogroups": [ { "orthogroup_id": "OG0001", "gene_family": "OG_DnaJ", "classification": "Single-Copy 1:1 Core Orthogroup", "member_count": 2, "species_count": 2, "is_single_copy_core": true, "mean_pident": 95.2507, "mean_raw_bit_score": 742.3, "mean_length_normalized_score": 904.7032, "members": [ "ECOLI_DnaJ", "SALMO_DnaJ" ] }, { "orthogroup_id": "OG0002", "gene_family": "OG_DnaK", "classification": "Single-Copy 1:1 Core Orthogroup", "member_count": 2, "species_count": 2, "is_single_copy_core": true, "mean_pident": 96.8652, "mean_raw_bit_score": 1199.5, "mean_length_normalized_score": 883.4046, "members": [ "ECOLI_DnaK", "SALMO_DnaK" ] }, { "orthogroup_id": "OG0003", "gene_family": "OG_IleS", "classification": "Single-Copy 1:1 Core Orthogroup", "member_count": 2, "species_count": 2, "is_single_copy_core": true, "mean_pident": 87.0899, "mean_raw_bit_score": 1693.3, "mean_length_normalized_score": 845.3546, "members": [ "ECOLI_IleS", "SALMO_IleS" ] }, { "orthogroup_id": "OG0004", "gene_family": "OG_NhaA", "classification": "Single-Copy 1:1 Core Orthogroup", "member_count": 2, "species_count": 2, "is_single_copy_core": true, "mean_pident": 93.2292, "mean_raw_bit_score": 709.9, "mean_length_normalized_score": 853.1034, "members": [ "ECOLI_NhaA", "SALMO_NhaA" ] }, { "orthogroup_id": "OG0005", "gene_family": "OG_RibF", "classification": "Single-Copy 1:1 Core Orthogroup", "member_count": 2, "species_count": 2, "is_single_copy_core": true, "mean_pident": 89.9676, "mean_raw_bit_score": 553.9, "mean_length_normalized_score": 823.6887, "members": [ "ECOLI_RibF", "SALMO_RibF" ] }, { "orthogroup_id": "OG0006", "gene_family": "OG_TalB", "classification": "Single-Copy 1:1 Core Orthogroup", "member_count": 2, "species_count": 2, "is_single_copy_core": true, "mean_pident": 94.5122, "mean_raw_bit_score": 620.2, "mean_length_normalized_score": 851.2603, "members": [ "ECOLI_TalB", "SALMO_TalB" ] }, { "orthogroup_id": "OG0007", "gene_family": "OG_ThrA", "classification": "Single-Copy 1:1 Core Orthogroup", "member_count": 2, "species_count": 2, "is_single_copy_core": true, "mean_pident": 94.5122, "mean_raw_bit_score": 1522.7, "mean_length_normalized_score": 868.658, "members": [ "ECOLI_ThrA", "SALMO_ThrA" ] }, { "orthogroup_id": "OG0008", "gene_family": "OG_ThrB", "classification": "Single-Copy 1:1 Core Orthogroup", "member_count": 2, "species_count": 2, "is_single_copy_core": true, "mean_pident": 93.5065, "mean_raw_bit_score": 584.7, "mean_length_normalized_score": 877.7874, "members": [ "ECOLI_ThrB", "SALMO_ThrB" ] }, { "orthogroup_id": "OG0009", "gene_family": "OG_ThrC", "classification": "Single-Copy 1:1 Core Orthogroup", "member_count": 2, "species_count": 2, "is_single_copy_core": true, "mean_pident": 93.4579, "mean_raw_bit_score": 797.0, "mean_length_normalized_score": 869.5818, "members": [ "ECOLI_ThrC", "SALMO_ThrC" ] }, { "orthogroup_id": "OG0010", "gene_family": "OG_YaaJ", "classification": "Single-Copy 1:1 Core Orthogroup", "member_count": 2, "species_count": 2, "is_single_copy_core": true, "mean_pident": 76.2605, "mean_raw_bit_score": 748.4, "mean_length_normalized_score": 728.6735, "members": [ "ECOLI_YaaJ", "SALMO_YaaJ" ] } ], "focal_hits": [ { "query_id": "ECOLI_ThrA", "subject_id": "SALMO_ThrA", "query_species": "Escherichia_coli_K12", "subject_species": "Salmonella_enterica_LT2", "pident": 94.5122, "align_length": 820, "mismatches": 45, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 820, "s_start_1based": 15, "s_end_1based": 834, "raw_sw_score": 3941, "bit_score": 1522.7, "length_normalized_score": 868.658, "e_value": 0.0, "query_len": 820, "subject_len": 834, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "SALMO_ThrA", "subject_id": "ECOLI_ThrA", "query_species": "Salmonella_enterica_LT2", 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"SALMO_RibF", "query_species": "Escherichia_coli_K12", "subject_species": "Salmonella_enterica_LT2", "pident": 90.0, "align_length": 309, "mismatches": 30, "gap_opens": 1, "q_start_1based": 1, "q_end_1based": 309, "s_start_1based": 1, "s_end_1based": 308, "raw_sw_score": 1426, "bit_score": 553.0, "length_normalized_score": 822.6155, "e_value": 1.03e-204, "query_len": 313, "subject_len": 312, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "SALMO_RibF", "subject_id": "ECOLI_RibF", "query_species": "Salmonella_enterica_LT2", "subject_species": "Escherichia_coli_K12", "pident": 90.0, "align_length": 309, "mismatches": 30, "gap_opens": 1, "q_start_1based": 1, "q_end_1based": 308, "s_start_1based": 1, "s_end_1based": 309, "raw_sw_score": 1426, "bit_score": 553.0, "length_normalized_score": 822.6155, "e_value": 1.02e-204, "query_len": 312, "subject_len": 313, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "ECOLI_IleS", "subject_id": "SALMO_IleS", "query_species": 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"rbh_jaccard_native_vs_diamond_fast": 1.0, "diamond_fast_twilight_recall_pct": 100.0, "orthogroup_rand_concordance_pct": 100.0, "native_speedup_vs_diamond_swipe": 0.3915, "supermatrix_phylogeny": null, "ascii_cohort_table": "+--------------------------------------------------------------------------------------------------+\n| COHORT-02-ENTERIC-SYNTENY-10LOCI — Enterobacterial thrLABC-dnaKJ-ileS 10-Gene Synteny & +31.4 kb Genomic Island Shift |\n+------------------------------+----------------------+----------------------+---------------------+\n| Metric | Native SW-BLOSUM62 | DIAMOND v2.2.8 SWIPE | DIAMOND v2.2.8 Fast |\n+------------------------------+----------------------+----------------------+---------------------+\n| Proteins / Species | 20 / 2 | 20 / 2 | 20 / 2 |\n| Cross-Species Hits | 20 | 20 | 20 |\n| Twilight Hits (<35% ID) | 0 | 0 | 0 |\n| 1:1 RBH Ortholog Pairs | 10 | 10 | 10 |\n| Co-Ortholog In-Paralog Pairs | 0 | 0 | 0 |\n| Out-Paralog Pairs Rejected | 0 | 0 | 0 |\n| Single-Copy Core Orthogroups | 10 | 10 | 10 |\n| Length Slope b (Raw -> Norm) | 0.4923 -> 0.0000 | 0.4927 -> 0.0000 | 0.4927 -> 0.0000 |\n| Wall-Clock Runtime (ms) | 387.21 | 151.58 | 263.07 |\n+------------------------------+----------------------+----------------------+---------------------+" }, { "cohort_id": "COHORT-03-VERTEBRATE-MITO-COX1-COX2", "cohort_title": "12-Taxon Vertebrate Mitogenome Complex IV (COX1 516 aa vs. COX2 227 aa) Length Normalization", "taxonomic_scope": "Eukaryota (12 Jawed Vertebrates across Mammalia & Aves; Mitochondrial Genetic Code icode = 1)", "biological_focus": "Emms & Kelly (2015) Gene-Length Normalization (2.45x Raw Bit-Score Disparity) & Concatenated Supermatrix Tree", "protein_count": 24, "species_count": 12, "native_result": { "engine_name": "bio-suite Native 4-Stage SW-BLOSUM62 + Length-Normalized RBH Engine", "engine_mode": "Native", "protein_count": 24, "species_count": 12, "total_all_vs_all_hits": 292, "cross_species_hits": 268, "twilight_zone_hits_under_35pct": 4, "rbh_ortholog_pairs_count": 132, "in_paralog_pairs_count": 0, "out_paralog_pairs_rejected": 2, "inferred_orthogroups_count": 2, "single_copy_core_orthogroups": 2, "length_bias_slope_raw_b": 0.6332, "length_bias_slope_normalized_b": 0.0, "wall_clock_ms": 313.1077, "orthogroups": [ { "orthogroup_id": "OG0001", "gene_family": "OG_COX1", "classification": "Single-Copy 1:1 Core Orthogroup", "member_count": 12, "species_count": 12, "is_single_copy_core": true, "mean_pident": 90.1455, "mean_raw_bit_score": 979.153, "mean_length_normalized_score": 586.5276, "members": [ "Anas_platyrhynchos_COX1", "Columba_livia_COX1", "Didelphis_virginiana_COX1", "Equus_caballus_COX1", "Gorilla_gorilla_COX1", "Mus_musculus_COX1", "Ornithorhynchus_anatinus_COX1", "Pan_troglodytes_COX1", "Pongo_pygmaeus_COX1", "Rattus_norvegicus_COX1", "Struthio_camelus_COX1", "Taeniopygia_guttata_COX1" ] }, { "orthogroup_id": "OG0002", "gene_family": "OG_COX2", "classification": "Single-Copy 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513, "mismatches": 55, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 513, "s_start_1based": 4, "s_end_1based": 516, "raw_sw_score": 2500, "bit_score": 967.0, "length_normalized_score": 580.1077, "e_value": 0.0, "query_len": 516, "subject_len": 516, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "Gorilla_gorilla_COX1", "subject_id": "Struthio_camelus_COX1", "query_species": "Gorilla_gorilla", "subject_species": "Struthio_camelus", "pident": 86.8, "align_length": 514, "mismatches": 68, "gap_opens": 0, "q_start_1based": 2, "q_end_1based": 515, "s_start_1based": 3, "s_end_1based": 516, "raw_sw_score": 2444, "bit_score": 946.0, "length_normalized_score": 567.5097, "e_value": 0.0, "query_len": 516, "subject_len": 516, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "Gorilla_gorilla_COX1", "subject_id": "Didelphis_virginiana_COX1", "query_species": "Gorilla_gorilla", "subject_species": "Didelphis_virginiana", "pident": 86.5, "align_length": 511, "mismatches": 69, "gap_opens": 0, "q_start_1based": 5, "q_end_1based": 515, "s_start_1based": 12, "s_end_1based": 522, "raw_sw_score": 2432, "bit_score": 941.0, "length_normalized_score": 560.3889, "e_value": 0.0, "query_len": 516, "subject_len": 522, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "Gorilla_gorilla_COX1", "subject_id": "Columba_livia_COX1", "query_species": "Gorilla_gorilla", "subject_species": "Columba_livia", "pident": 86.3, "align_length": 512, "mismatches": 70, "gap_opens": 0, "q_start_1based": 4, "q_end_1based": 515, "s_start_1based": 12, "s_end_1based": 523, "raw_sw_score": 2429, "bit_score": 940.0, "length_normalized_score": 559.1147, "e_value": 0.0, "query_len": 516, "subject_len": 523, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "Gorilla_gorilla_COX1", "subject_id": "Taeniopygia_guttata_COX1", "query_species": "Gorilla_gorilla", "subject_species": "Taeniopygia_guttata", "pident": 85.2, "align_length": 514, "mismatches": 76, "gap_opens": 0, "q_start_1based": 2, 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1, "s_end_1based": 227, "raw_sw_score": 1168, "bit_score": 454.0, "length_normalized_score": 771.2691, "e_value": 2.66e-168, "query_len": 227, "subject_len": 227, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "Gorilla_gorilla_COX2", "subject_id": "Pongo_pygmaeus_COX2", "query_species": "Gorilla_gorilla", "subject_species": "Pongo_pygmaeus", "pident": 97.4, "align_length": 227, "mismatches": 6, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 227, "s_start_1based": 10, "s_end_1based": 236, "raw_sw_score": 1166, "bit_score": 453.0, "length_normalized_score": 750.8369, "e_value": 7.45e-168, "query_len": 227, "subject_len": 236, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "Gorilla_gorilla_COX2", "subject_id": "Equus_caballus_COX2", "query_species": "Gorilla_gorilla", "subject_species": "Equus_caballus", "pident": 74.5, "align_length": 220, "mismatches": 56, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 220, "s_start_1based": 1, "s_end_1based": 220, "raw_sw_score": 885, "bit_score": 345.0, "length_normalized_score": 586.0966, "e_value": 3.57e-125, "query_len": 227, "subject_len": 227, "homology_class": "1:1 RBH Ortholog" } ] }, "bit_score_pearson_r": 1.0, "mean_abs_delta_bit_score": 0.4856, "rbh_jaccard_native_vs_diamond_swipe": 1.0, "rbh_jaccard_native_vs_diamond_fast": 1.0, "diamond_fast_twilight_recall_pct": 0.0, "orthogroup_rand_concordance_pct": 100.0, "native_speedup_vs_diamond_swipe": 0.402, "supermatrix_phylogeny": { "pipeline_chain": "OrthologyMode::Native -> AlignerMode::Native -> ModelTestMode::Native -> TreeBuilderMode::Native", "partitioned_loci_count": 2, "taxa_count": 12, "supermatrix_length_bp": 3902, "best_substitution_model_bic": "GTR+G", "supermatrix_ln_l": -18721.4092, "total_tree_length": 1.6406, "mean_branch_support_pct": 98.9628, "newick_tree": "(((Columba_livia:0.08938,Taeniopygia_guttata:0.14329)100:0.02200,(Didelphis_virginiana:0.13389,((Pongo_pygmaeus:0.09607,(Gorilla_gorilla:0.06512,Pan_troglodytes:0.04173)100:0.02289)100:0.10820,(Equus_caballus:0.12640,(Ornithorhynchus_anatinus:0.18935,(Mus_musculus:0.09331,Rattus_norvegicus:0.10225)100:0.04864)100:0.01937)100:0.02103)100:0.03289)100:0.05186)95:0.00366,(Anas_platyrhynchos:0.12766,Struthio_camelus:0.09794)95:0.00366);" }, "ascii_cohort_table": "+--------------------------------------------------------------------------------------------------+\n| COHORT-03-VERTEBRATE-MITO-COX1-COX2 — 12-Taxon Vertebrate Mitogenome Complex IV (COX1 516 aa vs. COX2 227 aa) Length Normalization |\n+------------------------------+----------------------+----------------------+---------------------+\n| Metric | Native SW-BLOSUM62 | DIAMOND v2.2.8 SWIPE | DIAMOND v2.2.8 Fast |\n+------------------------------+----------------------+----------------------+---------------------+\n| Proteins / Species | 24 / 12 | 24 / 12 | 24 / 12 |\n| Cross-Species Hits | 268 | 264 | 264 |\n| Twilight Hits (<35% ID) | 4 | 0 | 0 |\n| 1:1 RBH Ortholog Pairs | 132 | 132 | 132 |\n| Co-Ortholog In-Paralog Pairs | 0 | 0 | 0 |\n| Out-Paralog Pairs Rejected | 2 | 0 | 0 |\n| Single-Copy Core Orthogroups | 2 | 2 | 2 |\n| Length Slope b (Raw -> Norm) | 0.6332 -> 0.0000 | 0.6338 -> 0.0000 | 0.6338 -> 0.0000 |\n| Wall-Clock Runtime (ms) | 313.11 | 125.86 | 260.82 |\n+------------------------------+----------------------+----------------------+---------------------+" }, { "cohort_id": "COHORT-04-MAMMAL-GLOBIN-APOE-PARALOGS", "cohort_title": "Mammalian Globin (HBA1/HBA2/HBB/MB) & Apolipoprotein (APOE3/APOE4/APOA1) Gene Family Graph", "taxonomic_scope": "Eukaryota (Primates & Rodentia: Homo sapiens, Pan troglodytes, Macaca mulatta, Mus musculus)", "biological_focus": "Concerted-Evolution Tandem In-Paralogs (HBA1/HBA2 100%) vs. Ancient Out-Paralogs (HBB 43.4%, MB 26.4%, APOA1 20.8%)", "protein_count": 20, "species_count": 4, "native_result": { "engine_name": "bio-suite Native 4-Stage SW-BLOSUM62 + Length-Normalized RBH Engine", "engine_mode": "Native", "protein_count": 20, "species_count": 4, "total_all_vs_all_hits": 208, "cross_species_hits": 152, "twilight_zone_hits_under_35pct": 62, "rbh_ortholog_pairs_count": 30, "in_paralog_pairs_count": 2, "out_paralog_pairs_rejected": 62, "inferred_orthogroups_count": 5, "single_copy_core_orthogroups": 1, "length_bias_slope_raw_b": 0.3295, "length_bias_slope_normalized_b": 0.0, "wall_clock_ms": 66.4235, "orthogroups": [ { "orthogroup_id": "OG0001", "gene_family": "OG_APOE", "classification": "Multi-Copy Co-Ortholog / In-Paralog Group", "member_count": 5, "species_count": 4, "is_single_copy_core": false, "mean_pident": 88.2882, "mean_raw_bit_score": 544.01, "mean_length_normalized_score": 380.1248, "members": [ "CHIMP_APOE", "HUMAN_APOE3", "HUMAN_APOE4", "MACAQUE_APOE", "MOUSE_APOE" ] }, { "orthogroup_id": "OG0002", "gene_family": "OG_AlphaGlobin", "classification": "Multi-Copy Co-Ortholog / In-Paralog Group", "member_count": 5, "species_count": 4, "is_single_copy_core": false, "mean_pident": 93.7324, "mean_raw_bit_score": 271.91, "mean_length_normalized_score": 321.8964, "members": [ "CHIMP_HBA1", "HUMAN_HBA1", "HUMAN_HBA2", "MACAQUE_HBA1", "MOUSE_HBA1" ] }, { "orthogroup_id": "OG0003", "gene_family": "OG_BetaGlobin", "classification": "Single-Copy 1:1 Core Orthogroup", "member_count": 4, "species_count": 4, "is_single_copy_core": true, "mean_pident": 88.6621, "mean_raw_bit_score": 273.5667, "mean_length_normalized_score": 316.5547, "members": [ "CHIMP_HBB", "HUMAN_HBB", "MACAQUE_HBB", "MOUSE_HBB" ] }, { "orthogroup_id": "OG0004", "gene_family": "OG_APOA1", "classification": "Partial Clade-Restricted Orthogroup", "member_count": 3, "species_count": 3, "is_single_copy_core": false, "mean_pident": 77.2784, "mean_raw_bit_score": 412.4333, "mean_length_normalized_score": 322.7274, "members": [ "CHIMP_APOA1", "HUMAN_APOA1", "MOUSE_APOA1" ] }, { "orthogroup_id": "OG0005", "gene_family": "OG_Myoglobin", "classification": "Partial Clade-Restricted Orthogroup", "member_count": 3, "species_count": 3, "is_single_copy_core": false, "mean_pident": 89.1775, "mean_raw_bit_score": 282.6, "mean_length_normalized_score": 317.1335, "members": [ "CHIMP_MB", "HUMAN_MB", "MOUSE_MB" ] } ], "focal_hits": [ { "query_id": "HUMAN_HBA1", "subject_id": "HUMAN_HBA2", "query_species": "Homo_sapiens", "subject_species": "Homo_sapiens", "pident": 100.0, "align_length": 142, "mismatches": 0, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 142, "raw_sw_score": 733, "bit_score": 287.0, "length_normalized_score": 339.7604, "e_value": 7.808282102765439e-82, "query_len": 142, "subject_len": 142, "homology_class": "Lineage-Specific In-Paralog (Co-Ortholog)" }, { "query_id": "HUMAN_HBA1", "subject_id": "CHIMP_HBA1", "query_species": "Homo_sapiens", "subject_species": "Pan_troglodytes", "pident": 100.0, "align_length": 142, "mismatches": 0, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 142, "raw_sw_score": 733, "bit_score": 287.0, "length_normalized_score": 339.7604, "e_value": 7.808282102765439e-82, "query_len": 142, "subject_len": 142, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "HUMAN_HBA1", "subject_id": "MACAQUE_HBA1", "query_species": "Homo_sapiens", "subject_species": "Macaca_mulatta", "pident": 97.1831, "align_length": 142, "mismatches": 4, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 142, "raw_sw_score": 712, "bit_score": 278.9, "length_normalized_score": 330.1714, "e_value": 2.1263984912431554e-79, "query_len": 142, "subject_len": 142, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "HUMAN_HBA1", "subject_id": "MOUSE_HBA1", "query_species": "Homo_sapiens", "subject_species": "Mus_musculus", "pident": 85.9155, "align_length": 142, "mismatches": 20, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 142, "raw_sw_score": 648, "bit_score": 254.2, "length_normalized_score": 300.9307, "e_value": 5.608784607072883e-72, "query_len": 142, "subject_len": 142, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "HUMAN_HBA1", "subject_id": "HUMAN_HBB", "query_species": "Homo_sapiens", "subject_species": "Homo_sapiens", "pident": 42.069, "align_length": 145, "mismatches": 76, "gap_opens": 2, "q_start_1based": 3, "q_end_1based": 141, "s_start_1based": 4, "s_end_1based": 146, "raw_sw_score": 285, "bit_score": 114.4, "length_normalized_score": 133.895, "e_value": 6.936242093197307e-30, "query_len": 142, "subject_len": 147, "homology_class": "Ancient Out-Paralog (Excluded from Orthogroup)" }, { "query_id": "HUMAN_HBA1", "subject_id": "CHIMP_HBB", "query_species": "Homo_sapiens", "subject_species": "Pan_troglodytes", "pident": 42.069, "align_length": 145, "mismatches": 76, "gap_opens": 2, "q_start_1based": 3, "q_end_1based": 141, "s_start_1based": 4, "s_end_1based": 146, "raw_sw_score": 285, "bit_score": 114.4, "length_normalized_score": 133.895, "e_value": 6.936242093197307e-30, "query_len": 142, "subject_len": 147, "homology_class": "Cross-Species Out-Paralog" }, { "query_id": "HUMAN_HBA1", "subject_id": "MACAQUE_HBB", "query_species": "Homo_sapiens", "subject_species": "Macaca_mulatta", "pident": 42.7586, "align_length": 145, "mismatches": 75, "gap_opens": 3, "q_start_1based": 3, "q_end_1based": 141, "s_start_1based": 4, "s_end_1based": 146, "raw_sw_score": 277, "bit_score": 111.3, "length_normalized_score": 130.2667, "e_value": 5.871881142682498e-29, "query_len": 142, "subject_len": 147, "homology_class": "Cross-Species Out-Paralog" }, { "query_id": "HUMAN_HBA1", "subject_id": "MOUSE_HBB", "query_species": "Homo_sapiens", "subject_species": "Mus_musculus", "pident": 42.7586, "align_length": 145, "mismatches": 75, "gap_opens": 3, "q_start_1based": 3, "q_end_1based": 141, "s_start_1based": 4, "s_end_1based": 146, "raw_sw_score": 288, "bit_score": 115.5, "length_normalized_score": 135.1824, "e_value": 3.1135393779359032e-30, "query_len": 142, "subject_len": 147, "homology_class": "Cross-Species Out-Paralog" }, { "query_id": "HUMAN_HBA1", "subject_id": "HUMAN_MB", "query_species": "Homo_sapiens", "subject_species": "Homo_sapiens", "pident": 26.3514, "align_length": 148, "mismatches": 103, "gap_opens": 1, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 148, "raw_sw_score": 123, "bit_score": 51.99, "length_normalized_score": 59.9239, "e_value": 4.2276377090610706e-11, "query_len": 142, "subject_len": 154, "homology_class": "Ancient Out-Paralog (Excluded from Orthogroup)" }, { "query_id": "HUMAN_HBA1", "subject_id": "CHIMP_MB", "query_species": "Homo_sapiens", "subject_species": "Pan_troglodytes", "pident": 26.3514, "align_length": 148, "mismatches": 103, "gap_opens": 1, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 148, "raw_sw_score": 123, "bit_score": 51.99, "length_normalized_score": 59.9239, "e_value": 4.2276377090610706e-11, "query_len": 142, "subject_len": 154, "homology_class": "Cross-Species Out-Paralog" }, { "query_id": "HUMAN_HBA1", "subject_id": "MOUSE_MB", "query_species": "Homo_sapiens", "subject_species": "Mus_musculus", "pident": 24.3243, "align_length": 148, "mismatches": 106, "gap_opens": 1, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 148, "raw_sw_score": 102, "bit_score": 43.9, "length_normalized_score": 50.5994, "e_value": 1.1512958071643116e-8, "query_len": 142, "subject_len": 154, "homology_class": "Cross-Species Out-Paralog" }, { "query_id": "HUMAN_HBA2", "subject_id": "HUMAN_HBA1", "query_species": "Homo_sapiens", "subject_species": "Homo_sapiens", "pident": 100.0, "align_length": 142, "mismatches": 0, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 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100.0, "align_length": 142, "mismatches": 0, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 142, "raw_sw_score": 733, "bit_score": 286.0, "length_normalized_score": 372.4665, "e_value": 4.1e-105, "query_len": 142, "subject_len": 142, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "HUMAN_HBA2", "subject_id": "MACAQUE_HBA1", "query_species": "Homo_sapiens", "subject_species": "Macaca_mulatta", "pident": 97.2, "align_length": 142, "mismatches": 4, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 142, "raw_sw_score": 712, "bit_score": 278.0, "length_normalized_score": 362.0479, "e_value": 6.54e-102, "query_len": 142, "subject_len": 142, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "HUMAN_HBA2", "subject_id": "MOUSE_HBA1", "query_species": "Homo_sapiens", "subject_species": "Mus_musculus", "pident": 85.9, "align_length": 142, "mismatches": 20, "gap_opens": 0, "q_start_1based": 1, 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733, "bit_score": 286.0, "length_normalized_score": 372.4665, "e_value": 4.1e-105, "query_len": 142, "subject_len": 142, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "CHIMP_HBA1", "subject_id": "MACAQUE_HBA1", "query_species": "Pan_troglodytes", "subject_species": "Macaca_mulatta", "pident": 97.2, "align_length": 142, "mismatches": 4, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 142, "raw_sw_score": 712, "bit_score": 278.0, "length_normalized_score": 362.0479, "e_value": 6.54e-102, "query_len": 142, "subject_len": 142, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "CHIMP_HBA1", "subject_id": "MOUSE_HBA1", "query_species": "Pan_troglodytes", "subject_species": "Mus_musculus", "pident": 85.9, "align_length": 142, "mismatches": 20, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 142, "raw_sw_score": 648, "bit_score": 254.0, "length_normalized_score": 330.7919, "e_value": 3.77e-92, "query_len": 142, "subject_len": 142, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "MACAQUE_HBA1", "subject_id": "HUMAN_HBA1", "query_species": "Macaca_mulatta", "subject_species": "Homo_sapiens", "pident": 97.2, "align_length": 142, "mismatches": 4, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 142, "raw_sw_score": 712, "bit_score": 278.0, "length_normalized_score": 362.0479, "e_value": 6.54e-102, "query_len": 142, "subject_len": 142, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "MACAQUE_HBA1", "subject_id": "HUMAN_HBA2", "query_species": "Macaca_mulatta", "subject_species": "Homo_sapiens", "pident": 97.2, "align_length": 142, "mismatches": 4, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 142, "raw_sw_score": 712, "bit_score": 278.0, "length_normalized_score": 362.0479, "e_value": 6.54e-102, "query_len": 142, "subject_len": 142, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "MACAQUE_HBA1", "subject_id": "CHIMP_HBA1", "query_species": "Macaca_mulatta", "subject_species": "Pan_troglodytes", "pident": 97.2, "align_length": 142, "mismatches": 4, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 142, "raw_sw_score": 712, "bit_score": 278.0, "length_normalized_score": 362.0479, "e_value": 6.54e-102, "query_len": 142, "subject_len": 142, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "MACAQUE_HBA1", "subject_id": "MOUSE_HBA1", "query_species": "Macaca_mulatta", "subject_species": "Mus_musculus", "pident": 88.0, "align_length": 142, "mismatches": 17, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 142, "raw_sw_score": 660, "bit_score": 258.0, "length_normalized_score": 336.0013, "e_value": 5.57e-94, "query_len": 142, "subject_len": 142, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "MOUSE_HBA1", "subject_id": "MACAQUE_HBA1", "query_species": "Mus_musculus", "subject_species": "Macaca_mulatta", "pident": 88.0, "align_length": 142, "mismatches": 17, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 142, "raw_sw_score": 660, "bit_score": 258.0, "length_normalized_score": 336.0013, "e_value": 5.57e-94, "query_len": 142, "subject_len": 142, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "MOUSE_HBA1", "subject_id": "HUMAN_HBA1", "query_species": "Mus_musculus", "subject_species": "Homo_sapiens", "pident": 85.9, "align_length": 142, "mismatches": 20, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 142, "raw_sw_score": 648, "bit_score": 254.0, "length_normalized_score": 330.7919, "e_value": 3.77e-92, "query_len": 142, "subject_len": 142, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "MOUSE_HBA1", "subject_id": "HUMAN_HBA2", "query_species": "Mus_musculus", "subject_species": "Homo_sapiens", "pident": 85.9, "align_length": 142, "mismatches": 20, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 142, "raw_sw_score": 648, "bit_score": 254.0, "length_normalized_score": 330.7919, "e_value": 3.77e-92, "query_len": 142, "subject_len": 142, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "MOUSE_HBA1", "subject_id": "CHIMP_HBA1", "query_species": "Mus_musculus", "subject_species": "Pan_troglodytes", "pident": 85.9, "align_length": 142, "mismatches": 20, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 142, "s_start_1based": 1, "s_end_1based": 142, "raw_sw_score": 648, "bit_score": 254.0, "length_normalized_score": 330.7919, "e_value": 3.77e-92, "query_len": 142, "subject_len": 142, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "HUMAN_HBB", "subject_id": "CHIMP_HBB", "query_species": "Homo_sapiens", "subject_species": "Pan_troglodytes", "pident": 100.0, "align_length": 147, "mismatches": 0, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 147, "s_start_1based": 1, "s_end_1based": 147, "raw_sw_score": 780, "bit_score": 305.0, "length_normalized_score": 385.9358, "e_value": 4.05e-112, "query_len": 147, "subject_len": 147, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "HUMAN_HBB", "subject_id": "MACAQUE_HBB", "query_species": "Homo_sapiens", "subject_species": "Macaca_mulatta", "pident": 95.2, "align_length": 147, "mismatches": 7, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 147, "s_start_1based": 1, "s_end_1based": 147, "raw_sw_score": 746, "bit_score": 291.0, "length_normalized_score": 368.2207, "e_value": 6.21e-107, "query_len": 147, "subject_len": 147, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "HUMAN_HBB", "subject_id": "MOUSE_HBB", "query_species": "Homo_sapiens", "subject_species": "Mus_musculus", "pident": 80.3, "align_length": 147, "mismatches": 29, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 147, "s_start_1based": 1, "s_end_1based": 147, "raw_sw_score": 638, "bit_score": 250.0, "length_normalized_score": 316.3408, "e_value": 1.83e-90, "query_len": 147, "subject_len": 147, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "CHIMP_HBB", "subject_id": "HUMAN_HBB", "query_species": "Pan_troglodytes", "subject_species": "Homo_sapiens", "pident": 100.0, "align_length": 147, "mismatches": 0, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 147, "s_start_1based": 1, "s_end_1based": 147, "raw_sw_score": 780, "bit_score": 305.0, "length_normalized_score": 385.9358, "e_value": 4.05e-112, "query_len": 147, "subject_len": 147, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "CHIMP_HBB", "subject_id": "MACAQUE_HBB", "query_species": "Pan_troglodytes", "subject_species": "Macaca_mulatta", "pident": 95.2, "align_length": 147, "mismatches": 7, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 147, "s_start_1based": 1, "s_end_1based": 147, "raw_sw_score": 746, "bit_score": 291.0, "length_normalized_score": 368.2207, "e_value": 6.21e-107, "query_len": 147, "subject_len": 147, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "CHIMP_HBB", "subject_id": "MOUSE_HBB", "query_species": "Pan_troglodytes", "subject_species": "Mus_musculus", "pident": 80.3, "align_length": 147, "mismatches": 29, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 147, "s_start_1based": 1, "s_end_1based": 147, "raw_sw_score": 638, "bit_score": 250.0, "length_normalized_score": 316.3408, "e_value": 1.83e-90, "query_len": 147, "subject_len": 147, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "MACAQUE_HBB", "subject_id": "HUMAN_HBB", "query_species": "Macaca_mulatta", "subject_species": "Homo_sapiens", "pident": 95.2, "align_length": 147, "mismatches": 7, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 147, "s_start_1based": 1, "s_end_1based": 147, "raw_sw_score": 746, "bit_score": 291.0, "length_normalized_score": 368.2207, "e_value": 6.21e-107, "query_len": 147, "subject_len": 147, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "MACAQUE_HBB", "subject_id": "CHIMP_HBB", "query_species": "Macaca_mulatta", "subject_species": "Pan_troglodytes", "pident": 95.2, "align_length": 147, "mismatches": 7, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 147, "s_start_1based": 1, "s_end_1based": 147, "raw_sw_score": 746, "bit_score": 291.0, "length_normalized_score": 368.2207, "e_value": 6.21e-107, "query_len": 147, "subject_len": 147, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "MACAQUE_HBB", "subject_id": "MOUSE_HBB", "query_species": "Macaca_mulatta", "subject_species": "Mus_musculus", "pident": 81.0, "align_length": 147, "mismatches": 28, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 147, "s_start_1based": 1, "s_end_1based": 147, "raw_sw_score": 641, "bit_score": 251.0, "length_normalized_score": 317.6062, "e_value": 6.37e-91, "query_len": 147, "subject_len": 147, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "MOUSE_HBB", "subject_id": "MACAQUE_HBB", "query_species": "Mus_musculus", "subject_species": "Macaca_mulatta", "pident": 81.0, "align_length": 147, "mismatches": 28, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 147, "s_start_1based": 1, "s_end_1based": 147, "raw_sw_score": 641, "bit_score": 251.0, "length_normalized_score": 317.6062, "e_value": 6.37e-91, "query_len": 147, "subject_len": 147, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "MOUSE_HBB", "subject_id": "HUMAN_HBB", "query_species": "Mus_musculus", "subject_species": "Homo_sapiens", "pident": 80.3, "align_length": 147, "mismatches": 29, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 147, "s_start_1based": 1, "s_end_1based": 147, "raw_sw_score": 638, "bit_score": 250.0, "length_normalized_score": 316.3408, "e_value": 1.83e-90, "query_len": 147, "subject_len": 147, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "MOUSE_HBB", "subject_id": "CHIMP_HBB", "query_species": "Mus_musculus", "subject_species": "Pan_troglodytes", "pident": 80.3, "align_length": 147, "mismatches": 29, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 147, "s_start_1based": 1, "s_end_1based": 147, "raw_sw_score": 638, "bit_score": 250.0, "length_normalized_score": 316.3408, "e_value": 1.83e-90, "query_len": 147, "subject_len": 147, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "HUMAN_MB", "subject_id": "CHIMP_MB", "query_species": "Homo_sapiens", "subject_species": "Pan_troglodytes", "pident": 100.0, "align_length": 154, "mismatches": 0, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 154, "s_start_1based": 1, "s_end_1based": 154, "raw_sw_score": 809, "bit_score": 316.0, "length_normalized_score": 384.6721, "e_value": 2.59e-116, "query_len": 154, "subject_len": 154, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "HUMAN_MB", "subject_id": "MOUSE_MB", "query_species": "Homo_sapiens", "subject_species": "Mus_musculus", "pident": 83.8, "align_length": 154, "mismatches": 25, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 154, "s_start_1based": 1, "s_end_1based": 154, "raw_sw_score": 678, "bit_score": 265.0, "length_normalized_score": 322.5889, "e_value": 2.45e-96, "query_len": 154, "subject_len": 154, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "CHIMP_MB", "subject_id": "HUMAN_MB", "query_species": "Pan_troglodytes", "subject_species": "Homo_sapiens", "pident": 100.0, "align_length": 154, "mismatches": 0, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 154, "s_start_1based": 1, "s_end_1based": 154, "raw_sw_score": 809, "bit_score": 316.0, "length_normalized_score": 384.6721, "e_value": 2.59e-116, "query_len": 154, "subject_len": 154, "homology_class": "1:1 RBH Ortholog" }, { "query_id": "CHIMP_MB", "subject_id": "MOUSE_MB", "query_species": "Pan_troglodytes", "subject_species": "Mus_musculus", "pident": 83.8, "align_length": 154, "mismatches": 25, "gap_opens": 0, "q_start_1based": 1, "q_end_1based": 154, "s_start_1based": 1, "s_end_1based": 154, "raw_sw_score": 678, "bit_score": 265.0, "length_normalized_score": 322.5889, "e_value": 2.45e-96, "query_len": 154, "subject_len": 154, "homology_class": "1:1 RBH Ortholog" } ] }, "bit_score_pearson_r": 1.0, "mean_abs_delta_bit_score": 0.3051, "rbh_jaccard_native_vs_diamond_swipe": 1.0, "rbh_jaccard_native_vs_diamond_fast": 1.0, "diamond_fast_twilight_recall_pct": 0.0, "orthogroup_rand_concordance_pct": 100.0, "native_speedup_vs_diamond_swipe": 1.7374, "supermatrix_phylogeny": null, "ascii_cohort_table": "+--------------------------------------------------------------------------------------------------+\n| COHORT-04-MAMMAL-GLOBIN-APOE-PARALOGS — Mammalian Globin (HBA1/HBA2/HBB/MB) & Apolipoprotein (APOE3/APOE4/APOA1) Gene Family Graph |\n+------------------------------+----------------------+----------------------+---------------------+\n| Metric | Native SW-BLOSUM62 | DIAMOND v2.2.8 SWIPE | DIAMOND v2.2.8 Fast |\n+------------------------------+----------------------+----------------------+---------------------+\n| Proteins / Species | 20 / 4 | 20 / 4 | 20 / 4 |\n| Cross-Species Hits | 152 | 152 | 60 |\n| Twilight Hits (<35% ID) | 62 | 62 | 0 |\n| 1:1 RBH Ortholog Pairs | 30 | 30 | 30 |\n| Co-Ortholog In-Paralog Pairs | 2 | 2 | 2 |\n| Out-Paralog Pairs Rejected | 62 | 62 | 0 |\n| Single-Copy Core Orthogroups | 1 | 1 | 1 |\n| Length Slope b (Raw -> Norm) | 0.3295 -> 0.0000 | 0.3305 -> 0.0000 | 0.4161 -> 0.0000 |\n| Wall-Clock Runtime (ms) | 66.42 | 115.40 | 282.51 |\n+------------------------------+----------------------+----------------------+---------------------+" } ], "ascii_master_summary_table": "+------------------------------------------------------------------------------------------------------------------------+\n| TOOL PAIR 6 CALIBRATION: NATIVE 4-STAGE SW-BLOSUM62 + RBH ENGINE vs. DIAMOND v2.2.8 (4 COHORTS, 80 PROTEINS) |\n+-----------------------------------+----------+------------+--------------+---------------+---------------+-------------+\n| Cohort ID | Proteins | BitScore r | |Delta Bit| | RBH Jaccard | Fast Twilight | Speedup |\n| | (Taxa) | (vs SWIPE) | (bits) | (SWIPE / Fast)| Recall (%) | (vs DIAMOND)|\n+-----------------------------------+----------+------------+--------------+---------------+---------------+-------------+\n| COHORT-01-PROK-ORIC-PARALOGS | 16 ( 3) | 1.0000 | 0.4689 | 1.000 / 0.692 | 0.0% | 0.43x |\n| COHORT-02-ENTERIC-SYNTENY-10LOCI | 20 ( 2) | 1.0000 | 0.5900 | 1.000 / 1.000 | 100.0% | 0.39x |\n| COHORT-03-VERTEBRATE-MITO-COX1-2 | 24 (12) | 1.0000 | 0.4856 | 1.000 / 1.000 | 0.0% | 0.40x |\n| COHORT-04-MAMMAL-GLOBIN-APOE | 20 ( 4) | 1.0000 | 0.3051 | 1.000 / 1.000 | 0.0% | 1.74x |\n+-----------------------------------+----------+------------+--------------+---------------+---------------+-------------+\n| MEAN / TOTAL ACROSS 4 COHORTS | 80 (21) | 1.0000 | 0.4624 | 1.000 (100% ) | 69.2% avg | 0.74x |\n+-----------------------------------+----------+------------+--------------+---------------+---------------+-------------+", "ascii_focal_alignment_gyrb": "========================================================================================\nFOCAL ALIGNMENT SUMMARY: DNA Gyrase Subunit B (GyrB) GHKL ATPase Lid Focal Alignment (Residues 121–180: Housekeeping GyrB1 vs. Novobiocin-Resistant GyrB2 In-Paralog)\nFull Alignment: 643 bp | Highlighted Window: nt 121..180 (60 bp) | Taxa/Operons: 4\nWindow Conservation: 2 invariant (*) | 1 transition-only (:) | 0 transversion (.) | 57 gapped cols\n========================================================================================\n1-Based Coord 121 130 140 150 160 170 1\nPosition Scale |...:....|....:....|....:....|....:....|....:....|....:....|\nGHKL-ATPase-Lid EEEEEEE-----[Arg138_Novobiocin_Anchor]-----HHHHHHHHHHHH-----[ATP_Mg2+_Loop]-----EEEE\n-------------------------------------------------------------------------------------------\nBacillus_subtilis_GyrB_WT GLHGVGASVVNALSTELDVTVHRDGKIHRQTYKRGVPVTDLEIIGETDHTGTTTHFVPDP\nStaphylococcus_aureus_GyrB_WT GGLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKAD\nPseudomonas_aeruginosa_GyrB1 GVSVVNALSHELRLTIRRHNKVWEQVYHHGVPQFPLREVGETDGSGTEVHFKPSPETFSN\nPseudomonas_aeruginosa_GyrB2 GVSIVNALSHELKLTIRKHNKIWEQVYHHGIPQFPLREVAETDGSGTEIHFKPSPETYSN\n-------------------------------------------------------------------------------------------\nClustal Conservation * : * \nColumn Entropy (0-2b) ▁▁▁▁▁▁▄▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▅▁▁▁▁▁▁▁▁▁▁▅▅▁▁▁▁▁▁▁▁\n\nFOCAL REGION DIAGNOSTIC CALLOUTS:\n • Residues 134-142 (GHKL ATP-Binding Lid): Conserved Gly-X-Gly-X-Gly motif + Arg138 novobiocin salt-bridge anchor (mutated to Lys138 in GyrB2 resistance paralog).\n • Native SW-BLOSUM62 & DIAMOND --swipe both score PSEUD_GyrB1 vs. PSEUD_GyrB2 at 1,498 bits (89.8% ID) > cross-phylum RBH (692 bits), grouping GyrB2 as a lineage-specific in-paralog.\n", "ascii_supermatrix_cladogram": "12-Taxon Vertebrate Complex IV Concatenated Supermatrix Cladogram (OG_COX1 + OG_COX2 = 2,229 bp; GTR+F+I+G4)\n============================================================================================================\n+-- Ornithorhynchus_anatinus (Platypus | Monotremata Outgroup) [NC_000891.1]\n|\n+-- Didelphis_virginiana (Virginia Opossum | Marsupialia) [NC_000886.1]\n|\n| +-- Equus_caballus (Horse | Laurasiatheria) [NC_001640.1]\n| |\n| +-----+ +-- Mus_musculus (House Mouse | Rodentia) [NC_005089.1]\n| | | +--+\n| | | | +-- Rattus_norvegicus (Brown Rat | Rodentia) [NC_001665.2]\n+--+ +--+\n| | +-- Pongo_pygmaeus (Bornean Orangutan | Hominidae) [NC_001646.1]\n| +--+\n| | +-- Gorilla_gorilla (Western Gorilla | Homininae) [NC_001645.1]\n| +--+\n| +-- Pan_troglodytes (Chimpanzee | Homininae) [NC_001643.1]\n|\n| +-- Struthio_camelus (Ostrich | Palaeognathae) [NC_000878.1]\n+--+\n| +-- Anas_platyrhynchos (Mallard Duck | Galloanserae) [NC_002785.1]\n+--+\n| +-- Columba_livia (Rock Dove | Columbiformes) [NC_013978.1]\n+--+\n+-- Taeniopygia_guttata (Zebra Finch | Passeriformes) [NC_010195.2]" }