{ "analysis": { "authors": "Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group", "citation": "Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353. v2.2 adds support for multiple-hit models", "contact": "spond@temple.edu", "info": "aBSREL (Adaptive branch-site random effects likelihood)\n uses an adaptive random effects branch-site model framework\n to test whether each branch has evolved under positive selection,\n using a procedure which infers an optimal number of rate categories per branch.", "requirements": "in-frame codon alignment and a phylogenetic tree", "version": "2.2" }, "branch attributes": { "0": { "BLTXBLABR": { "Baseline MG94xREV": 0.2757280099940251, "Baseline MG94xREV omega ratio": 0.5341465712333542, "Corrected P-value": 0.2651604063153776, "Full adaptive model": 0.5413009136338867, "Full adaptive model (non-synonymous subs/site)": 0.4452112971853568, "Full adaptive model (synonymous subs/site)": 0.09608961644852987, "LRT": 3.874602152918669, "Nucleotide GTR": 0.2605186300720645, "Rate Distributions": [ [ 0.350690353472359, 0.8801075834540383 ], [ 10.14663150845139, 0.1198924165459617 ] ], "Rate classes": 2, "Uncorrected P-value": 0.05303208126307551, "original name": "BLTXBLABR" }, "CALUKLK1B": { "Baseline MG94xREV": 0.1019778334651919, "Baseline MG94xREV omega ratio": 0.1799141178066999, "Corrected P-value": null, "Full adaptive model": 0.1077214479900578, "Full adaptive model (non-synonymous subs/site)": 0.04155101135453353, "Full adaptive model (synonymous subs/site)": 0.06617043663552417, "LRT": null, "Nucleotide GTR": 0.09481639860899553, "Rate Distributions": [ [ 0.206699903463952, 1 ] ], "Rate classes": 1, "Uncorrected P-value": null, "original name": "CALUKLK1B" }, "CALUKLK2": { "Baseline MG94xREV": 0.2199388651903933, "Baseline MG94xREV omega ratio": 0.4713460243392435, "Corrected P-value": null, "Full adaptive model": 0.252050733669911, "Full adaptive model (non-synonymous subs/site)": 0.1627469358585362, "Full adaptive model (synonymous subs/site)": 0.08930379781137476, "LRT": null, "Nucleotide GTR": 0.2185915104182697, "Rate Distributions": [ [ 0.04900112013258084, 0.6218837867871166 ], [ 1.505909067342557, 0.3781162132128834 ] ], "Rate classes": 2, "Uncorrected P-value": null, "original name": "CALUKLK2" }, "EREUK1A": { "Baseline MG94xREV": 0.2472771304618316, "Baseline MG94xREV omega ratio": 0.4355795426785534, "Corrected P-value": null, "Full adaptive model": 23.01351356365685, "Full adaptive model (non-synonymous subs/site)": 22.92143055167013, "Full adaptive model (synonymous subs/site)": 0.09208301198672826, "LRT": null, "Nucleotide GTR": 0.2275932672648502, "Rate Distributions": [ [ 0.3231786444572205, 0.9092995457262807 ], [ 900.1503203666465, 0.09070045427371931 ] ], "Rate classes": 2, "Uncorrected P-value": null, "original name": "EREUK1A" }, "EREUK1B": { "Baseline MG94xREV": 0.2011887065368257, "Baseline MG94xREV omega ratio": 0.2472357484371754, "Corrected P-value": null, "Full adaptive model": 43.80589365135502, "Full adaptive model (non-synonymous subs/site)": 43.70507439259794, "Full adaptive model (synonymous subs/site)": 0.1008192587570862, "LRT": null, "Nucleotide GTR": 0.1753161713238943, "Rate Distributions": [ [ 0.1061819817237521, 0.9084439472184237 ], [ 1557.508055951417, 0.0915560527815763 ] ], "Rate classes": 2, "Uncorrected P-value": null, "original name": "EREUK1B" }, "HOSAKLK1": { "Baseline MG94xREV": 0.137791700052647, "Baseline MG94xREV omega ratio": 0.4506696371137874, "Corrected P-value": null, "Full adaptive model": 0.1589720532267733, "Full adaptive model (non-synonymous subs/site)": 0.1043354553480508, "Full adaptive model (synonymous subs/site)": 0.0546365978787225, "LRT": null, "Nucleotide GTR": 0.1271907159420856, "Rate Distributions": [ [ 0.2275376959633997, 0.8997510138474988 ], [ 4.228150054516294, 0.1002489861525012 ] ], "Rate classes": 2, "Uncorrected P-value": null, "original name": "HOSAKLK1" }, "HOSAKLK2": { "Baseline MG94xREV": 0.05713654127027281, "Baseline MG94xREV omega ratio": 0.3815123365349325, "Corrected P-value": null, "Full adaptive model": 0.05292141328812448, "Full adaptive model (non-synonymous subs/site)": 0.02753045803628929, "Full adaptive model (synonymous subs/site)": 0.0253909552518352, "LRT": null, "Nucleotide GTR": 0.05693091948740823, "Rate Distributions": [ [ 0.3569086487747675, 1 ] ], "Rate classes": 1, "Uncorrected P-value": null, "original name": "HOSAKLK2" }, "HOSAKLK3": { "Baseline MG94xREV": 0.09906877042575744, "Baseline MG94xREV omega ratio": 0.8704025910134031, "Corrected P-value": null, "Full adaptive model": 0.1567538039938848, "Full adaptive model (non-synonymous subs/site)": 0.1294496030114319, "Full adaptive model (synonymous subs/site)": 0.02730420098245286, "LRT": null, "Nucleotide GTR": 0.09919428928776691, "Rate Distributions": [ [ 0.2444427596609231, 0.8791492608684942 ], [ 11.1352788354224, 0.1208507391315058 ] ], "Rate classes": 2, "Uncorrected P-value": null, "original name": "HOSAKLK3" }, "Node10": { "Baseline MG94xREV": 0.02713154601870469, "Baseline MG94xREV omega ratio": 10000000000, "Corrected P-value": 0.3161634765517561, "Full adaptive model": 0.06854554060367514, "Full adaptive model (non-synonymous subs/site)": 0.04749110034516905, "Full adaptive model (synonymous subs/site)": 0.02105444025850608, "LRT": 2.558976030368285, "Nucleotide GTR": 0.04651424848415949, "Rate Distributions": [ [ 0, 0.9216234349949541 ], [ 9.473380506492733, 0.07837656500504586 ] ], "Rate classes": 2, "Uncorrected P-value": 0.105387825517252 }, "Node12": { "Baseline MG94xREV": 0.05351811374161557, "Baseline MG94xREV omega ratio": 0.3201391694190276, "Corrected P-value": null, "Full adaptive model": 0.2321223274364063, "Full adaptive model (non-synonymous subs/site)": 0.2070771319200576, "Full adaptive model (synonymous subs/site)": 0.02504519551634873, "LRT": null, "Nucleotide GTR": 0.05222724832977575, "Rate Distributions": [ [ 0.1053010179645542, 0.9526862283471769 ], [ 55.40288307511457, 0.04731377165282313 ] ], "Rate classes": 2, "Uncorrected P-value": null }, "Node13": { "Baseline MG94xREV": 0.01463038269486094, "Baseline MG94xREV omega ratio": 10000000000, "Corrected P-value": null, "Full adaptive model": 0.004523777835621262, "Full adaptive model (non-synonymous subs/site)": 0.004523777835621262, "Full adaptive model (synonymous subs/site)": 1e-10, "LRT": null, "Nucleotide GTR": 0.01601992976692079, "Rate Distributions": [ [ 10000000000, 1 ] ], "Rate classes": 1, "Uncorrected P-value": null }, "Node15": { "Baseline MG94xREV": 0.02407954696223161, "Baseline MG94xREV omega ratio": 0.4258115942303968, "Corrected P-value": null, "Full adaptive model": 0.02622325004715084, "Full adaptive model (non-synonymous subs/site)": 0.01963189136735891, "Full adaptive model (synonymous subs/site)": 0.00659135867979193, "LRT": null, "Nucleotide GTR": 0.02388063171194447, "Rate Distributions": [ [ 0, 0.9537306148924308 ], [ 21.18927728666248, 0.04626938510756917 ] ], "Rate classes": 2, "Uncorrected P-value": null }, "Node18": { "Baseline MG94xREV": 0.03862345094199512, "Baseline MG94xREV omega ratio": 0.6331244462923122, "Corrected P-value": null, "Full adaptive model": 0.5405804718654943, "Full adaptive model (non-synonymous subs/site)": 0.53529334024339, "Full adaptive model (synonymous subs/site)": 0.005287131622104178, "LRT": null, "Nucleotide GTR": 0.03619247678248119, "Rate Distributions": [ [ 0.814144090285984, 0.9518869350632223 ], [ 676.5706283914558, 0.04811306493677769 ] ], "Rate classes": 2, "Uncorrected P-value": null }, "Node20": { "Baseline MG94xREV": 0.02029654475641261, "Baseline MG94xREV omega ratio": 10000000000, "Corrected P-value": null, "Full adaptive model": 0.01516182990729437, "Full adaptive model (non-synonymous subs/site)": 0.01516182990729437, "Full adaptive model (synonymous subs/site)": 1e-10, "LRT": null, "Nucleotide GTR": 0.02097890300141165, "Rate Distributions": [ [ 10000000000, 1 ] ], "Rate classes": 1, "Uncorrected P-value": null }, "Node22": { "Baseline MG94xREV": 0.09777491984692198, "Baseline MG94xREV omega ratio": 0.5074106111279888, "Corrected P-value": null, "Full adaptive model": 0.1291093126599494, "Full adaptive model (non-synonymous subs/site)": 0.09208194108992553, "Full adaptive model (synonymous subs/site)": 0.03702737157002384, "LRT": null, "Nucleotide GTR": 0.09288220748481305, "Rate Distributions": [ [ 0, 0.8106486649474107 ], [ 4.323205551917483, 0.1893513350525893 ] ], "Rate classes": 2, "Uncorrected P-value": null }, "Node3": { "Baseline MG94xREV": 0.1674490783676515, "Baseline MG94xREV omega ratio": 0.268768755075537, "Corrected P-value": 0.4170743300211868, "Full adaptive model": 1071.969076220746, "Full adaptive model (non-synonymous subs/site)": 1071.907882820363, "Full adaptive model (synonymous subs/site)": 0.0611934003827738, "LRT": 2.579217568149033, "Nucleotide GTR": 0.1249005467507917, "Rate Distributions": [ [ 0.2779189877013303, 0.9423424974362009 ], [ 100000, 0.05765750256379909 ] ], "Rate classes": 2, "Uncorrected P-value": 0.1042685825052967 }, "Node5": { "Baseline MG94xREV": 0.02592981993923705, "Baseline MG94xREV omega ratio": 0.7166201270444271, "Corrected P-value": 0.2078532235343459, "Full adaptive model": 24.71864207839139, "Full adaptive model (non-synonymous subs/site)": 24.7151782732591, "Full adaptive model (synonymous subs/site)": 0.003463805132287321, "LRT": 4.700059961891384, "Nucleotide GTR": 0.02565992430960325, "Rate Distributions": [ [ 0.937023378711337, 0.9765218569309077 ], [ 100000, 0.02347814306909235 ] ], "Rate classes": 2, "Uncorrected P-value": 0.03464220392239098 }, "Node7": { "Baseline MG94xREV": 0.03310122139558106, "Baseline MG94xREV omega ratio": 1.081826443969445, "Corrected P-value": 0.1696379312329145, "Full adaptive model": 0.04073643372350181, "Full adaptive model (non-synonymous subs/site)": 0.03499766282235768, "Full adaptive model (synonymous subs/site)": 0.005738770901144118, "LRT": 5.396372090841396, "Nucleotide GTR": 0.03341116258581665, "Rate Distributions": [ [ 0, 0.8714919051035224 ], [ 15.62112634707516, 0.1285080948964776 ] ], "Rate classes": 2, "Uncorrected P-value": 0.02423399017613065 }, "ORANA14": { "Baseline MG94xREV": 0.6011476478977805, "Baseline MG94xREV omega ratio": 0.2521734672412525, "Corrected P-value": null, "Full adaptive model": 0.705990082151869, "Full adaptive model (non-synonymous subs/site)": 0.4253859345801481, "Full adaptive model (synonymous subs/site)": 0.2806041475717211, "LRT": null, "Nucleotide GTR": 0.4475650286696786, "Rate Distributions": [ [ 0, 0.5339472132073233 ], [ 1.070721703309376, 0.4660527867926767 ] ], "Rate classes": 2, "Uncorrected P-value": null, "original name": "ORANA14" }, "SOPAB2": { "Baseline MG94xREV": 0.05238806444684669, "Baseline MG94xREV omega ratio": 1.094125787630194, "Corrected P-value": 0.05930477484743424, "Full adaptive model": 0.1400444553504092, "Full adaptive model (non-synonymous subs/site)": 0.1299724407180069, "Full adaptive model (synonymous subs/site)": 0.01007201463240225, "LRT": 7.719880734366598, "Nucleotide GTR": 0.05217210713234858, "Rate Distributions": [ [ 0.9463488243185192, 0.980493705459657 ], [ 170.1936651364374, 0.01950629454034303 ] ], "Rate classes": 2, "Uncorrected P-value": 0.00741309685592928, "original name": "SOPAB2" }, "SOPAB3": { "Baseline MG94xREV": 0.02928920305251104, "Baseline MG94xREV omega ratio": 1.758754504781475, "Corrected P-value": 0.001050229533765878, "Full adaptive model": 0.4971506803287252, "Full adaptive model (non-synonymous subs/site)": 0.4937437260477939, "Full adaptive model (synonymous subs/site)": 0.003406954280931216, "LRT": 15.94149784824913, "Nucleotide GTR": 0.02939078077942028, "Rate Distributions": [ [ 1, 0.9765526101088804 ], [ 1992.878315093416, 0.02344738989111961 ] ], "Rate classes": 2, "Uncorrected P-value": 0.0001166921704184309, "original name": "SOPAB3" }, "SOPAB5": { "Baseline MG94xREV": 0.04078566872162188, "Baseline MG94xREV omega ratio": 0.5952693661682016, "Corrected P-value": 1, "Full adaptive model": 0.04040289336473817, "Full adaptive model (non-synonymous subs/site)": 0.02488540506850383, "Full adaptive model (synonymous subs/site)": 0.01551748829623434, "LRT": 0, "Nucleotide GTR": 0.03746701465910655, "Rate Distributions": [ [ 0.5278930727151008, 1 ] ], "Rate classes": 1, "Uncorrected P-value": 1, "original name": "SOPAB5" }, "SOPAB7": { "Baseline MG94xREV": 0.06990284481002289, "Baseline MG94xREV omega ratio": 0.6042955451938858, "Corrected P-value": 1, "Full adaptive model": 0.0687644988621514, "Full adaptive model (non-synonymous subs/site)": 0.04429359814703517, "Full adaptive model (synonymous subs/site)": 0.02447090071511615, "LRT": 0, "Nucleotide GTR": 0.07024162527393263, "Rate Distributions": [ [ 0.5958180851426135, 1 ] ], "Rate classes": 1, "Uncorrected P-value": 1, "original name": "SOPAB7" } }, "attributes": { "Baseline MG94xREV": { "attribute type": "branch length", "display order": 1 }, "Baseline MG94xREV omega ratio": { "attribute type": "branch label", "display order": 1 }, "Corrected P-value": { "attribute type": "branch label", "display order": 6 }, "Full adaptive model": { "attribute type": "branch length", "display order": 2 }, "Full adaptive model (non-synonymous subs/site)": { "attribute type": "branch label", "display order": 10 }, "Full adaptive model (synonymous subs/site)": { "attribute type": "branch label", "display order": 9 }, "LRT": { "attribute type": "branch label", "display order": 4 }, "Nucleotide GTR": { "attribute type": "branch length", "display order": 0 }, "Rate Distributions": { "attribute type": "branch label", "display order": 3 }, "Rate classes": { "attribute type": "branch label", "display order": 2 }, "Uncorrected P-value": { "attribute type": "branch label", "display order": 5 }, "original name": { "attribute type": "node label", "display order": -1 } } }, "data partitions": { "0": { "coverage": [ [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269 ] ], "name": "absrel.filter.default" } }, "fits": { "Baseline MG94xREV": { "AIC-c": 13403.34370889033, "Equilibrium frequencies": [ [ 0.00983779315685237 ], [ 0.02887163305452133 ], [ 0.024358456885313 ], [ 0.01245080300903158 ], [ 0.007218501851835066 ], [ 0.02118462274482766 ], [ 0.01787307004030712 ], [ 0.00913580344133645 ], [ 0.007229986816642212 ], [ 0.02121832844327743 ], [ 0.01790150690776549 ], [ 0.009150338920188211 ], [ 0.008223532374136169 ], [ 0.02413415339523172 ], [ 0.02036153389145479 ], [ 0.01040777946804515 ], [ 0.01019805103655125 ], [ 0.02992890607722369 ], [ 0.02525045836271011 ], [ 0.01290674875022231 ], [ 0.007482841844583661 ], [ 0.02196039909533534 ], [ 0.01852757803958801 ], [ 0.009470354607908715 ], [ 0.007494747386343775 ], [ 0.02199533908924788 ], [ 0.018557056259046 ], [ 0.009485422372884819 ], [ 0.008524676369492267 ], [ 0.02501794092683252 ], [ 0.02110716890432788 ], [ 0.01078891012445867 ], [ 0.01260397826619493 ], [ 0.03698974248866722 ], [ 0.03120755399971847 ], [ 0.01595171274903268 ], [ 0.009248196115166838 ], [ 0.02714130297274692 ], [ 0.0228986097538858 ], [ 0.01170460347996127 ], [ 0.009262910415875271 ], [ 0.02718448602040145 ], [ 0.02293504248363416 ], [ 0.01172322603652608 ], [ 0.01053582055064527 ], [ 0.0309201809813046 ], [ 0.02608677846164425 ], [ 0.01333423300562279 ], [ 0.02386190601918906 ], [ 0.01029037362396173 ], [ 0.005965967095195416 ], [ 0.01750872477613074 ], [ 0.01477178366636951 ], [ 0.007550583741324454 ], [ 0.01753658195370017 ], [ 0.01479528624613319 ], [ 0.007562597063523778 ], [ 0.006796607461962263 ], [ 0.01994646091137985 ], [ 0.0168284560560505 ], [ 0.008601849956528428 ] ], "Log Likelihood": -6737.783534385442, "display order": 1, "estimated parameters": 60, "branch-annotations": { "BLTXBLABR": { "LRT": 3.874602152918669, "omegas": [ { "omega": 0.5341465712333542, "prop": 1 } ], "p": 0.2651604063153776, "uncorrected p": 0.05303208126307551, "tested": true }, "CALUKLK1B": { "LRT": "test not run", "omegas": [ { "omega": 0.1799141178066999, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": false }, "CALUKLK2": { "LRT": "test not run", "omegas": [ { "omega": 0.4713460243392435, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": false }, "EREUK1A": { "LRT": "test not run", "omegas": [ { "omega": 0.4355795426785534, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": false }, "EREUK1B": { "LRT": "test not run", "omegas": [ { "omega": 0.2472357484371754, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": false }, "HOSAKLK1": { "LRT": "test not run", "omegas": [ { "omega": 0.4506696371137874, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": false }, "HOSAKLK2": { "LRT": "test not run", "omegas": [ { "omega": 0.3815123365349325, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": false }, "HOSAKLK3": { "LRT": "test not run", "omegas": [ { "omega": 0.8704025910134031, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": false }, "Node10": { "LRT": 2.558976030368285, "omegas": [ { "omega": 10000000000, "prop": 1 } ], "p": 0.3161634765517561, "uncorrected p": 0.105387825517252, "tested": true }, "Node12": { "LRT": "test not run", "omegas": [ { "omega": 0.3201391694190276, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": false }, "Node13": { "LRT": "test not run", "omegas": [ { "omega": 10000000000, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": false }, "Node15": { "LRT": "test not run", "omegas": [ { "omega": 0.4258115942303968, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": false }, "Node18": { "LRT": "test not run", "omegas": [ { "omega": 0.6331244462923122, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": false }, "Node20": { "LRT": "test not run", "omegas": [ { "omega": 10000000000, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": false }, "Node22": { "LRT": "test not run", "omegas": [ { "omega": 0.5074106111279888, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": false }, "Node3": { "LRT": 2.579217568149033, "omegas": [ { "omega": 0.268768755075537, "prop": 1 } ], "p": 0.4170743300211868, "uncorrected p": 0.1042685825052967, "tested": true }, "Node5": { "LRT": 4.700059961891384, "omegas": [ { "omega": 0.7166201270444271, "prop": 1 } ], "p": 0.2078532235343459, "uncorrected p": 0.03464220392239098, "tested": true }, "Node7": { "LRT": 5.396372090841396, "omegas": [ { "omega": 1.081826443969445, "prop": 1 } ], "p": 0.1696379312329145, "uncorrected p": 0.02423399017613065, "tested": true }, "ORANA14": { "LRT": "test not run", "omegas": [ { "omega": 0.2521734672412525, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": false }, "SOPAB2": { "LRT": 7.719880734366598, "omegas": [ { "omega": 1.094125787630194, "prop": 1 } ], "p": 0.05930477484743424, "uncorrected p": 0.00741309685592928, "tested": true }, "SOPAB3": { "LRT": 15.94149784824913, "omegas": [ { "omega": 1.758754504781475, "prop": 1 } ], "p": 0.001050229533765878, "uncorrected p": 0.0001166921704184309, "tested": true }, "SOPAB5": { "LRT": 0, "omegas": [ { "omega": 0.5952693661682016, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": true }, "SOPAB7": { "LRT": 0, "omegas": [ { "omega": 0.6042955451938858, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": true } }, "annotation-tag": "ω" }, "Full adaptive model": { "AIC-c": 13403.34370889033, "Log Likelihood": -6605.056920330964, "display order": 2, "estimated parameters": 94, "branch-annotations": { "BLTXBLABR": { "LRT": 3.874602152918669, "omegas": [ { "omega": 0.350690353472359, "prop": 0.8801075834540383 }, { "omega": 10.14663150845139, "prop": 0.1198924165459617 } ], "p": 0.2651604063153776, "uncorrected p": 0.05303208126307551, "tested": true }, "CALUKLK1B": { "LRT": "test not run", "omegas": [ { "omega": 0.206699903463952, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": false }, "CALUKLK2": { "LRT": "test not run", "omegas": [ { "omega": 0.04900112013258084, "prop": 0.6218837867871166 }, { "omega": 1.505909067342557, "prop": 0.3781162132128834 } ], "p": 1, "uncorrected p": 1, "tested": false }, "EREUK1A": { "LRT": "test not run", "omegas": [ { "omega": 0.3231786444572205, "prop": 0.9092995457262807 }, { "omega": 900.1503203666465, "prop": 0.09070045427371931 } ], "p": 1, "uncorrected p": 1, "tested": false }, "EREUK1B": { "LRT": "test not run", "omegas": [ { "omega": 0.1061819817237521, "prop": 0.9084439472184237 }, { "omega": 1557.508055951417, "prop": 0.0915560527815763 } ], "p": 1, "uncorrected p": 1, "tested": false }, "HOSAKLK1": { "LRT": "test not run", "omegas": [ { "omega": 0.2275376959633997, "prop": 0.8997510138474988 }, { "omega": 4.228150054516294, "prop": 0.1002489861525012 } ], "p": 1, "uncorrected p": 1, "tested": false }, "HOSAKLK2": { "LRT": "test not run", "omegas": [ { "omega": 0.3569086487747675, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": false }, "HOSAKLK3": { "LRT": "test not run", "omegas": [ { "omega": 0.2444427596609231, "prop": 0.8791492608684942 }, { "omega": 11.1352788354224, "prop": 0.1208507391315058 } ], "p": 1, "uncorrected p": 1, "tested": false }, "Node10": { "LRT": 2.558976030368285, "omegas": [ { "omega": 0, "prop": 0.9216234349949541 }, { "omega": 9.473380506492733, "prop": 0.07837656500504586 } ], "p": 0.3161634765517561, "uncorrected p": 0.105387825517252, "tested": true }, "Node12": { "LRT": "test not run", "omegas": [ { "omega": 0.1053010179645542, "prop": 0.9526862283471769 }, { "omega": 55.40288307511457, "prop": 0.04731377165282313 } ], "p": 1, "uncorrected p": 1, "tested": false }, "Node13": { "LRT": "test not run", "omegas": [ { "omega": 10000000000, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": false }, "Node15": { "LRT": "test not run", "omegas": [ { "omega": 0, "prop": 0.9537306148924308 }, { "omega": 21.18927728666248, "prop": 0.04626938510756917 } ], "p": 1, "uncorrected p": 1, "tested": false }, "Node18": { "LRT": "test not run", "omegas": [ { "omega": 0.814144090285984, "prop": 0.9518869350632223 }, { "omega": 676.5706283914558, "prop": 0.04811306493677769 } ], "p": 1, "uncorrected p": 1, "tested": false }, "Node20": { "LRT": "test not run", "omegas": [ { "omega": 10000000000, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": false }, "Node22": { "LRT": "test not run", "omegas": [ { "omega": 0, "prop": 0.8106486649474107 }, { "omega": 4.323205551917483, "prop": 0.1893513350525893 } ], "p": 1, "uncorrected p": 1, "tested": false }, "Node3": { "LRT": 2.579217568149033, "omegas": [ { "omega": 0.2779189877013303, "prop": 0.9423424974362009 }, { "omega": 100000, "prop": 0.05765750256379909 } ], "p": 0.4170743300211868, "uncorrected p": 0.1042685825052967, "tested": true }, "Node5": { "LRT": 4.700059961891384, "omegas": [ { "omega": 0.937023378711337, "prop": 0.9765218569309077 }, { "omega": 100000, "prop": 0.02347814306909235 } ], "p": 0.2078532235343459, "uncorrected p": 0.03464220392239098, "tested": true }, "Node7": { "LRT": 5.396372090841396, "omegas": [ { "omega": 0, "prop": 0.8714919051035224 }, { "omega": 15.62112634707516, "prop": 0.1285080948964776 } ], "p": 0.1696379312329145, "uncorrected p": 0.02423399017613065, "tested": true }, "ORANA14": { "LRT": "test not run", "omegas": [ { "omega": 0, "prop": 0.5339472132073233 }, { "omega": 1.070721703309376, "prop": 0.4660527867926767 } ], "p": 1, "uncorrected p": 1, "tested": false }, "SOPAB2": { "LRT": 7.719880734366598, "omegas": [ { "omega": 0.9463488243185192, "prop": 0.980493705459657 }, { "omega": 170.1936651364374, "prop": 0.01950629454034303 } ], "p": 0.05930477484743424, "uncorrected p": 0.00741309685592928, "tested": true }, "SOPAB3": { "LRT": 15.94149784824913, "omegas": [ { "omega": 1, "prop": 0.9765526101088804 }, { "omega": 1992.878315093416, "prop": 0.02344738989111961 } ], "p": 0.001050229533765878, "uncorrected p": 0.0001166921704184309, "tested": true }, "SOPAB5": { "LRT": 0, "omegas": [ { "omega": 0.5278930727151008, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": true }, "SOPAB7": { "LRT": 0, "omegas": [ { "omega": 0.5958180851426135, "prop": 1 } ], "p": 1, "uncorrected p": 1, "tested": true } }, "annotation-tag": "ω" }, "Nucleotide GTR": { "AIC-c": 13403.34370889033, "Equilibrium frequencies": [ [ 0.2182625761801467 ], [ 0.2945976655304204 ], [ 0.2858175808284268 ], [ 0.2013221774610061 ] ], "Log Likelihood": -6918.575782024222, "display order": 0, "estimated parameters": 31 } }, "input": { "file name": "/home/datamonkey/datamonkey-js-server/production/app/absrel/output/5ff5719adf8ae6122221918b", "number of sequences": 13, "number of sites": 270, "partition count": 1, "trees": { "0": "((SOPAB7:0.0827561900145955,(SOPAB5:0.05037261895600794,(SOPAB2:0.04568405144732782,SOPAB3:0.03551713848053199)Node7:0.01554095470959638)Node5:0.004603485675018344)Node3:0.1336958814817678,(BLTXBLABR:0.2359278658277936,((EREUK1B:0.1527635743228616,(CALUKLK1B:0.09867767106092942,HOSAKLK1:0.1224715348673463)Node15:0.01956539114448527)Node13:0.01078209228478759,(EREUK1A:0.2014129280260493,(CALUKLK2:0.2051444986973396,(HOSAKLK2:0.0666197573578389,HOSAKLK3:0.08873107157661153)Node22:0.07849227005798634)Node20:0.02270753503945207)Node18:0.01535169095177221)Node12:0.0172454242674482)Node10:0.01896231157195738,ORANA14:0.197806456257949)" } }, "test results": { "P-value threshold": 0.05, "positive test results": 1, "tested": 9 }, "tested": { "0": { "BLTXBLABR": "test", "CALUKLK1B": "background", "CALUKLK2": "background", "EREUK1A": "background", "EREUK1B": "background", "HOSAKLK1": "background", "HOSAKLK2": "background", "HOSAKLK3": "background", "Node10": "test", "Node12": "background", "Node13": "background", "Node15": "background", "Node18": "background", "Node20": "background", "Node22": "background", "Node3": "test", "Node5": "test", "Node7": "test", "ORANA14": "background", "SOPAB2": "test", "SOPAB3": "test", "SOPAB5": "test", "SOPAB7": "test" } }, "timers": { "Baseline model fitting": { "order": 2, "timer": 7 }, "Complexity analysis": { "order": 3, "timer": 103 }, "Full adaptive model fitting": { "order": 4, "timer": 74 }, "Overall": { "order": 0, "timer": 345 }, "Preliminary model fitting": { "order": 1, "timer": 1 }, "Testing for selection": { "order": 5, "timer": 160 } }, "trees": { "branchLengths": { "Baseline MG94xREV": { "BLTXBLABR": 0.2757280099940251, "CALUKLK1B": 0.1019778334651919, "CALUKLK2": 0.2199388651903933, "EREUK1A": 0.2472771304618316, "EREUK1B": 0.2011887065368257, "HOSAKLK1": 0.137791700052647, "HOSAKLK2": 0.05713654127027281, "HOSAKLK3": 0.09906877042575744, "Node10": 0.02713154601870469, "Node12": 0.05351811374161557, "Node13": 0.01463038269486094, "Node15": 0.02407954696223161, "Node18": 0.03862345094199512, "Node20": 0.02029654475641261, "Node22": 0.09777491984692198, "Node3": 0.1674490783676515, "Node5": 0.02592981993923705, "Node7": 0.03310122139558106, "ORANA14": 0.6011476478977805, "SOPAB2": 0.05238806444684669, "SOPAB3": 0.02928920305251104, "SOPAB5": 0.04078566872162188, "SOPAB7": 0.06990284481002289 }, "Full adaptive model": { "BLTXBLABR": 0.5413009136338867, "CALUKLK1B": 0.1077214479900578, "CALUKLK2": 0.252050733669911, "EREUK1A": 23.01351356365685, "EREUK1B": 43.80589365135502, "HOSAKLK1": 0.1589720532267733, "HOSAKLK2": 0.05292141328812448, "HOSAKLK3": 0.1567538039938848, "Node10": 0.06854554060367514, "Node12": 0.2321223274364063, "Node13": 0.004523777835621262, "Node15": 0.02622325004715084, "Node18": 0.5405804718654943, "Node20": 0.01516182990729437, "Node22": 0.1291093126599494, "Node3": 1071.969076220746, "Node5": 24.71864207839139, "Node7": 0.04073643372350181, "ORANA14": 0.705990082151869, "SOPAB2": 0.1400444553504092, "SOPAB3": 0.4971506803287252, "SOPAB5": 0.04040289336473817, "SOPAB7": 0.0687644988621514 } } } }