Mercurial > repos > iuc > hyphy_cfel

comparison test-data/summary/nsp8.PRIME.json @ 13:fea3f6a79104 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
author iuc
date Tue, 07 Oct 2025 20:41:29 +0000
parents 8aec341d10ec
children
comparison
equal deleted inserted replaced
12:8aec341d10ec 13:fea3f6a79104
1 {
2 "MLE":{
3 "content":{
4 "0": [
5 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
6 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
7 [3.250710398632764, 2.543979863949704, 0.000260278000831112, -9.279879778998792, -9.280586210458985, 1, -0.03083220306091588, 1, -9.279441534952744, 0.246012012715961, 1, -9.279441534952742, 0.3671614662852546, 1, -9.279441534952742, -0.1712639841078613, 1, -9.279441534952737, 0.2624930750589453, 1, -9.279441534952737],
8 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
9 [0, 0.5537159057721711, 1.458738094193731e-05, -9.653318580984834, -9.653547984340634, 1, 0.5104924519363182, 1, -9.653308651005229, -0.1367278481442925, 1, -9.653308651005229, 0.5919809397222774, 1, -9.653308651005229, -0.1178049485056483, 1, -9.653308651005229, 0.6168893659032167, 1, -9.653308651005229],
10 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
11 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
12 [3.120608327772482, 2.614421539287396, 0.0002691437601083932, -9.281874472112623, -9.282601939787694, 1, 0.04953574496877388, 1, -9.281318510005244, -0.3536675776484469, 1, -9.28131851006073, 0.880962199708396, 1, -9.281317114729157, 0.4033925671419755, 1, -9.281318509947875, 0.1204188200792286, 1, -9.281318509962372],
13 [0, 1.464518485321612, 2.65544170203544e-05, -10.62328331507694, -10.62393719801913, 1, -0.09951441286794899, 1, -10.62316666528899, 1.323879892092505, 1, -10.62316613327963, 0.2196172646873195, 1, -10.62316666528898, 0.1504288706197217, 1, -10.62316666528886, 0.1853325884628318, 1, -10.62316666528886],
14 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
15 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
16 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
17 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
18 [6.642049096285556, 0.9469109242998108, 0.0003620738332646705, -9.286905212837395, -9.287223838078173, 1, 0.4022344790431069, 1, -9.286810976596435, 1.197779080102599, 1, -9.286810976596437, 0.3589760978791438, 1, -9.286810976596435, 0.1410881301787622, 1, -9.286810976596435, -0.7850618321090115, 1, -9.286810976596435],
19 [0, 0.3704419203686217, 2.210275222817499e-05, -16.66016944635797, -16.66043872464428, 1, 0.3930843395219109, 1, -16.6601383462611, 0.2146143946643995, 1, -16.6601383462611, 1.161538175214766, 1, -16.66013834626109, -0.02607298415665098, 1, -16.66013834627073, -0.8791189616882017, 1, -16.66013834626112],
20 [6.642049096285556, 0.9469109242998108, 0.0003620738332646705, -9.286905212837395, -9.287223838078173, 1, 0.4022344790431069, 1, -9.286810976596435, 1.197779080102599, 1, -9.286810976596437, 0.3589760978791438, 1, -9.286810976596435, 0.1410881301787622, 1, -9.286810976596435, -0.7850618321090115, 1, -9.286810976596435],
21 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
22 [6.15200979587571, 0.7664418907442996, 0.0003241434681835816, -8.397013750003021, -8.397276621570359, 1, -0.2520353509836328, 1, -8.396847261582421, 0.1107366238822934, 1, -8.396847261582423, 0.1524040518249381, 1, -8.396847261582419, 0.5017067831730544, 1, -8.396847261582419, 0.1728359761835464, 1, -8.396847261582433],
23 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
24 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
25 [0, 1.640491119619624, 4.530322293875232e-05, -9.354648574415357, -9.354308225168079, 1, 0.3464427721141255, 1, -9.353594756043833, 0.2276891704052981, 1, -9.353594756041785, 0.3556536075671364, 1, -9.353594755979932, 0.1068123231090358, 1, -9.353594756061817, 0.2571589515668457, 1, -9.353594756037198],
26 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
27 [0, 0.5015980633927689, 4.463668663386787e-06, -8.522225370219248, -8.522470343311889, 1, 0.6345463979548933, 1, -8.522216760929579, 0.1722685944219224, 1, -8.522216760929579, 1.128111851533095, 1, -8.522216760929581, -0.6910734187295019, 1, -8.522216760929579, 2.390142475570945, 1, -8.522216760929579],
28 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
29 [6.301467504498501, 0.7526223661612935, 0.0003001909030794377, -8.672366005775045, -8.672432133233857, 1, 0.2618940269421511, 1, -8.672102287956223, 0.6582503354300704, 1, -8.672102287956223, 1.050277083425478, 1, -8.672102287956221, -0.08424846335836793, 1, -8.672102287956221, -0.1357766893320302, 1, -8.672102287956221],
30 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
31 [0, 0.5512309724476928, 8.513742052958957e-06, -9.420046721686061, -9.420342676134863, 1, 0.6795819760143671, 1, -9.4200272421609, 1.040207016685132, 1, -9.4200272421609, -0.08929739409055948, 1, -9.4200272421609, 0.3064415455843166, 1, -9.4200272421609, 0.4137989676898545, 1, -9.420027242160906],
32 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
33 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
34 [21.2877137100817, 0, 0.0009669236379089351, -15.3926323423968, -15.39183141405638, 1, -0.1787030911977786, 1, -15.39173843488844, -0.1086019453788971, 1, -15.39173843488844, -0.4050978384688558, 1, -15.39173843488844, 0.2124526460287185, 1, -15.39173843488844, -0.6731357797187441, 1, -15.39173843488844],
35 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
36 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
37 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
38 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
39 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
40 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
41 [11.87187552899661, 3358.908612242396, 0.07528426938276855, -8.01868320319551, -8.544833620740533, 1, 1.572130801493356, 1, -8.018303255019214, -3.41347440280111, 1, -8.027628651067467, 0.604745149073098, 1, -8.018524792468007, 15, 1, -8.039312402027347, 0.83611296255941, 1, -8.019736577345743],
42 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
43 [0, 2.099036995031509, 6.570131831507147e-05, -6.675948222507397, -6.676160312892713, 1, 0.01467357592763005, 1, -6.67541631192989, 1.061527192923924, 1, -6.675413146527749, -0.08361893300410453, 1, -6.675416311817156, -0.2532585366996872, 1, -6.675416311846627, 0.48406220510454, 1, -6.675416312965201],
44 [16.35523177357988, 0.5510526648388852, 0.0009405310582744312, -8.145123184049975, -8.143971341698274, 1, -0.141220056164769, 1, -8.143661715012232, 0.1914003202153734, 1, -8.143661715012234, -0.5992493819694997, 1, -8.143661715012227, 0.2087929580717243, 1, -8.143661715012227, 0.3698721224741515, 1, -8.143661715012227],
45 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
46 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
47 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
48 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
49 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
50 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
51 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
52 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
53 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
54 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
55 [0, 1.487855228882824, 1.564123866710565e-05, -10.67669066061746, -10.67905353362621, 1, 0.1618805399867843, 1, -10.67665866469908, 0.4220048705165958, 1, -10.67665866469908, 0.4271525136220899, 1, -10.67665866469908, -0.1588840789214494, 1, -10.6766586646991, 1.618475173402782, 1, -10.6766586646991],
56 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
57 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
58 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
59 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
60 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
61 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
62 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
63 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
64 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
65 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
66 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
67 [6.340767690830408, 0.7526223661612935, 0.0003922450590121044, -8.67489030380119, -8.674637993132928, 1, -0.6857370610916009, 1, -8.674309828870351, 0.1185655057742294, 1, -8.674309828870355, -0.2459746692025252, 1, -8.674309828870351, 0.04449224604253502, 1, -8.674309828870351, 0.5914251547638932, 1, -8.674309828870349],
68 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
69 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
70 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
71 [1.056087079762036, 0.8222444849370368, 0.0001264691661837167, -11.33016032130324, -11.32696268541853, 1, -0.1727875502949552, 1, -11.32498564106033, 0.3186283160044413, 1, -11.32498564122183, -0.3449112262681385, 1, -11.32498564105286, 0.6352356008790669, 1, -11.32498564133693, 0.3382958499338234, 1, -11.32498564121247],
72 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
73 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
74 [1.138928232279054, 0.9171597633136092, 0.0002430871379490812, -10.68239019164284, -10.68005440892361, 1, 0.2575107646025272, 1, -10.23609175803548, -0.4590553134523093, 1, -10.23609175870073, -0.01966378774215988, 1, -10.2360917582697, 0.2091468335218698, 1, -10.23609175809283, -0.04074479375795732, 1, -10.23609175829752],
75 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
76 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
77 [16.13920664252111, 1.103507670905478, 0.0008515183148219861, -9.066901725357468, -9.066446358094618, 1, -0.6357574465966143, 1, -9.065889573593365, 0.2807163127061337, 1, -9.065889573593365, 0.2031819770094125, 1, -9.065889573593365, 0.3001855321622762, 1, -9.065889573593363, -0.0814314415956256, 1, -9.065889573593363],
78 [0, 0.3002103330212254, 4.89258789742326e-06, -8.073097387694396, -8.07313472507207, 1, -0.2933150298713428, 1, -8.072985279600863, 0.9221122812122359, 1, -8.072985279600863, 0.5197219092866691, 1, -8.072985279600863, 0.28651806815879, 1, -8.072985279600863, 0.3893442450269322, 1, -8.072985279600861],
79 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
80 [0, 1.507974392107734, 2.060562652030412e-05, -9.638128885821633, -9.638686027367106, 1, 0.3594160579861987, 1, -9.63788451830893, 0.2576042076908743, 1, -9.63788451830893, 0.2787933154180046, 1, -9.637884518308928, 0.7064358243826948, 1, -9.637884518308928, 0.6579205240578683, 1, -9.637884518308928],
81 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
82 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
83 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
84 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
85 [0.5049260216636672, 1.266997878275074, 0.0006242229177028295, -13.80059823578676, -13.7608099535438, 1, -0.2409631373193451, 1, -13.76022644299233, -0.288144673453706, 1, -13.76022644300942, -0.2869762055871761, 1, -13.7602264430103, 0.05773058590485474, 1, -13.76022644298499, 0.06759963226787809, 1, -13.76022644298417],
86 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
87 [0, 1.358147735140135, 2.862590185840447e-05, -8.927507579657542, -8.928062245292038, 1, -0.2004553720026996, 1, -8.92734125059032, 0.671631263016662, 1, -8.927341250590322, 0.847778171343791, 1, -8.927341250590368, 0.3328138335272307, 1, -8.92734125059032, 0.00795309362672247, 1, -8.927341250590324],
88 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
89 [0, 0.4757903077559259, 2.391708943848935e-05, -12.65464060498691, -12.69173819589251, 1, -0.3074071969443506, 1, -12.65462191342067, 0.6866130010821937, 1, -12.65462191342067, 0.191735016509868, 1, -12.65462191342067, -0.3440428884464239, 1, -12.65462191342067, 0.2788189333211322, 1, -12.65462191342067],
90 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
91 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
92 [0, 0, 0, -9.358354051238528, -9.358363162987645, 1, -0.2595474939699753, 1, -9.358353684562129, -0.4165608331875593, 1, -9.358353684562129, 0.2480911331244882, 1, -9.358353684562129, 0.7506375700332563, 1, -9.358353684562129, 0.3806075909167843, 1, -9.358353684562129],
93 [0, 1.561936054228835, 5.304618931137966e-05, -8.509593072010237, -8.50986790405153, 1, -0.6400244441468755, 1, -8.509339173601399, 0.4732846676756352, 1, -8.509339173601399, 0.1327537716102745, 1, -8.509339173601399, 0.4343561916421816, 1, -8.509339173601399, 0.7295929086587101, 1, -8.509339173601377],
94 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
95 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
96 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
97 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
98 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
99 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
100 [0, 0.07513120524573011, 4.026982534009169e-07, -8.464103009985886, -8.464242348410973, 1, 7.712515808112293, 1, -8.464100150969795, -0.002712850932269675, 1, -8.464100150969745, 0.1624977107040588, 1, -8.464100150969793, 0.4715862624215356, 1, -8.464100150969745, -0.08783874051398359, 1, -8.464100150969744],
101 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
102 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
103 [19.6825530061475, 0.600388814460612, 0.0009339020162382645, -7.337229447807304, -7.336832893418913, 1, 0.4458852126452318, 1, -7.336487462356399, 0.7585335755706408, 1, -7.336487462356399, 0.08507875931696018, 1, -7.336487462356399, -0.267050703624337, 1, -7.336487462356399, -0.2147616367584433, 1, -7.336487462356399],
104 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
105 [20.32596835494961, 0.600388814460612, 0.001266336117564567, -7.340073811518233, -7.338795266687233, 1, 0.7948874889375515, 1, -7.338466266483618, -0.5434939739527445, 1, -7.338466266483618, -0.3894707452134489, 1, -7.338466266483618, -0.09230748723528348, 1, -7.338466266483618, 0.097990386036515, 1, -7.338466266483618],
106 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
107 [3.285931987915582, 1.501479279648968, 0.0002734480936310624, -10.86444166853046, -10.86406980605987, 1, 0.02165175319452921, 1, -10.86331519852894, 0.03576648984913484, 1, -10.86331519857565, -0.1299089615204276, 1, -10.86331519872217, -0.422045393053767, 1, -10.86331519883445, 0.6945791190785982, 1, -10.86331519752498],
108 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
109 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
110 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
111 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
112 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
113 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
114 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
115 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
116 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
117 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
118 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
119 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
120 [3.151961146536734, 2.634772693661995, 0.0005718898774090106, -10.83830323071386, -10.8385140518685, 1, 0.05799295277549382, 1, -10.83718210281268, 0.1785567718945754, 1, -10.83718210281268, -0.007731414747369366, 1, -10.83718210281268, -0.004193123511904951, 1, -10.83718210281268, -0.2151248944303416, 1, -10.83718210281268],
121 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
122 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
123 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
124 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
125 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
126 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
127 [0, 1.447730777049217, 1.485978466892902e-05, -9.204623895518683, -9.204766179922879, 1, -0.5720526862655848, 1, -9.204275595496901, 0.7230336131147019, 1, -9.204275595496901, 0.6255678193451613, 1, -9.204275595496901, 0.5123037767720485, 1, -9.204275595496901, 1.399743574526714, 1, -9.204275595496902],
128 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
129 [0, 0.05482783084407766, 3.994670349027644e-08, -7.421698122236018, -7.421831641929532, 1, -0.5485463071655138, 1, -7.421697015208141, 0.1736059152840212, 1, -7.421697015208175, 0.3496925965429374, 1, -7.421697015208141, 0.4848689203421276, 1, -7.421697015208141, 12.94252706739861, 1, -7.421697015208172],
130 [0, 1.555343860730179, 7.135140672589343e-05, -8.458196108214208, -8.45862605736893, 1, -0.005484939061168711, 1, -8.457893808970253, 0.1028295149917871, 1, -8.457893808970249, 0.2639525132305186, 1, -8.457893808970248, 0.3088551097090368, 1, -8.457893808970248, 0.1694843461681877, 1, -8.457893808970248],
131 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
132 [5.13830842872464, 1.499789961783057, 0.0004865892182211683, -10.02730702519262, -10.02737457492912, 1, -0.3407622719247865, 1, -10.02679879831546, 0.4568437778437747, 1, -10.02679879831548, -0.3469120653980059, 1, -10.02679879831561, -0.4377908796730941, 1, -10.02679879831548, 0.4385130897356323, 1, -10.02679879831546],
133 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
134 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
135 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
136 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
137 [0, 2738.750253750779, 110.3592534216164, -5.845964514154565, -7.246578373749505, 1, 0.5629652821575621, 1, -5.845756765958907, 1.202368481239023, 1, -5.847166207717827, -5.291865349182212, 1, -5.866781004648637, -0.05781161548817493, 1, -5.84587950347407, 10.9797065564442, 1, -5.856877812393424],
138 [0, 2.909535478858993, 6.442081096845745e-05, -7.911249250781965, -7.912077516619656, 1, 0.7341747605162299, 1, -7.911060904782952, 0.2758374750973312, 1, -7.911060904782952, 0.4500632018221016, 1, -7.91105926975087, 0.474082513850355, 1, -7.911060904782952, -0.1241173654426523, 1, -7.911060904782952],
139 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
140 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
141 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
142 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
143 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
144 [0, 1.576919603187598, 1.454189061286498e-05, -9.381670616935986, -9.382033288215027, 1, 0.5749106680865744, 1, -9.381642262347425, 0.7192339333470378, 1, -9.381642262347425, -0.3947896157946159, 1, -9.381642262347169, 0.1727687900245574, 1, -9.381642262347169, 1.857922955151209, 1, -9.381642262347423],
145 [3.895491407178215, 2.491129766976171, 0.0002684692929920988, -8.329401161502417, -8.329908616851093, 1, -0.199572708988974, 1, -8.329129136549167, 0.1244023255435259, 1, -8.329129136549167, 0.809449893125575, 1, -8.329129136549167, 0.3022347051020699, 1, -8.329129136548939, 0.09118744848040194, 1, -8.329129136549168],
146 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
147 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
148 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
149 [0, 1.172480822570774, 0.0003023190020661169, -8.107274227472981, -8.107305626649916, 1, 1.467912966335734, 1, -8.106883281078112, 1.048361211127534, 1, -8.106883281078114, -0.5416160389560009, 1, -8.106883281078112, 0.1135946638146065, 1, -8.106883281078114, -0.1325696557631366, 1, -8.106883281078112],
150 [0, 1.447730777049217, 5.547512828790685e-05, -9.204558610686396, -9.204761318800728, 1, -0.5469336186589974, 1, -9.204270178268578, 0.1679731510120776, 1, -9.204270178268578, 0.6101716407459336, 1, -9.204270178268578, 0.6366720169799334, 1, -9.20427017826858, 0.3026022637982405, 1, -9.204270178268576],
151 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
152 [0, 0.8021912340588233, 0.0001593478246306375, -7.810592067432045, -7.810274302358139, 1, 1.214628584235453, 1, -7.809987625626755, 0.402932476852712, 1, -7.809987625626755, -0.5860606765531364, 1, -7.8099887494883, -0.2741674810072515, 1, -7.809987625626755, 0.3464840553661773, 1, -7.809987625626755],
153 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
154 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
155 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
156 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
157 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
158 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
159 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
160 [4.025656470392913, 0.7757847450990134, 0.0002523869337258775, -8.593435159167299, -8.593437290531689, 1, 0.1563465020213214, 1, -8.59309040227874, 0.6915518508377344, 1, -8.593090402278738, -0.04593557256507134, 1, -8.593090402278742, -0.1173882156008064, 1, -8.593090402291411, -0.1227425497076833, 1, -8.593090402278776],
161 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
162 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
163 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
164 [14.09104806652614, 1.242379135936382, 0.0007324602434091573, -9.290221181705286, -9.290422612612275, 1, -0.2456989986751775, 1, -9.289764218025159, -0.03353577849673799, 1, -9.289764218025162, 0.4572122013800251, 1, -9.289764218025299, 0.1408979936005787, 1, -9.289764218025159, 0.003684470590371985, 1, -9.289764218025159],
165 [0, 0.1355031069705359, 3.874368591754749e-06, -6.700570027803357, -6.700513534170148, 1, 0.1080208297227145, 1, -6.700359604735913, -0.05966663280547952, 1, -6.700359604735913, 3.354290516476016, 1, -6.700383228459372, -0.3699225637235463, 1, -6.700359604735913, 0.1301105054525743, 1, -6.700359604735913],
166 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
167 [21.49266025712136, 0, 0.0009762326535946639, -11.0106564649928, -11.00989211870829, 1, -0.257396164503197, 1, -11.00983371279438, -0.6465147990453251, 1, -11.00983371279438, -0.6390438825746161, 1, -11.00983371279438, 0.08429415135394877, 1, -11.00983371279438, -0.3944275495847627, 1, -11.00983371279438],
168 [0, 1.603811733757937, 6.075748055809287e-05, -7.988062375946436, -7.988973025165929, 1, 1.543284254272088, 1, -7.987981906240607, -0.2215986708775382, 1, -7.987981906240607, 0.2101565622838899, 1, -7.987981906240607, 0.07009767212145024, 1, -7.987981906240607, 0.03340199705111992, 1, -7.987981906240607],
169 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
170 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
171 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
172 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
173 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
174 [0, 0.008996126907272754, 2.671287508671499e-07, -14.79407131133979, -14.79406886215786, 1, 0.5126526720917212, 1, -14.79406748881603, 0.6116236716776852, 1, -14.79406748881603, -0.3909299113702913, 1, -14.79406748881603, 0.4498998160193369, 1, -14.79406748881603, 0.7265221606822454, 1, -14.79406748881603],
175 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
176 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
177 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
178 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
179 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
180 [20.61615174164107, 1.915676726331523, 0.001718090369725785, -7.275968408597492, -7.275925155280767, 1, -0.03904887988100746, 1, -7.275245166724103, 0.08053731644779075, 1, -7.275245166724103, -0.6491116795318861, 1, -7.275245166724102, -0.8941363847829037, 1, -7.275245166724102, 0.8684223541229297, 1, -7.275245166724103],
181 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
182 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
183 [20.84433848557291, 1.915676726331523, 0.001607541332969535, -7.276015218332248, -7.275923445607657, 1, 0.07057282939330427, 1, -7.275258359363819, -1.106882638559168, 1, -7.275258359363819, 0.5461137346786853, 1, -7.275258359363819, -0.0388985643327846, 1, -7.275258359363819, 0.1622348741957941, 1, -7.275258359363819],
184 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
185 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
186 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
187 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
188 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
189 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
190 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
191 [15.0944976053826, 0, 0.0006856173817337676, -14.16674063926069, -14.16530148666303, 1, -0.3667952979382496, 1, -14.16527177829697, -0.1231919975472201, 1, -14.16527177829697, 0.2433684497128029, 1, -14.16527177829697, -0.02022659549827326, 1, -14.16527177829697, -0.5755422053010966, 1, -14.16527177829697],
192 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
193 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
194 [0, 2.82801162274558, 2.790863870994061e-05, -9.190253720392601, -9.192071264649048, 1, 0.01737633505219859, 1, -9.190226194505639, -0.1088228686156002, 1, -9.190226194505637, 0.2873400520012543, 1, -9.190226194505637, 0.1912073989428711, 1, -9.190226194505637, 2.889196848047757, 1, -9.190226194505637],
195 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
196 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
197 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
198 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
199 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
200 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
201 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
202 [0, 1.231388513343972, 0.000158458220515845, -13.77233562678079, -13.77239892102621, 1, 0.03644798756061563, 1, -13.77190817477141, -0.3104805457700024, 1, -13.77191376864584, 0.2357212180710769, 1, -13.77190817477141, -0.03138277695602196, 1, -13.77191376864584, -0.005528760550374304, 1, -13.7719081747714]
203 ]
204 },
205 "headers": [
206 ["alpha;", "Synonymous substitution rate at a site"],
207 ["β", "Log of property independent non-synonymous rate a site"],
208 ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"],
209 ["PRIME LogL", "Site Log-likelihood under the PRIME model"],
210 ["FEL LogL", "Site Log-likelihood under the FEL model"],
211 ["p-value", "Omnibus p-value (any property is important)"],
212 ["λ1", "Importance for Factor I bipolar"],
213 ["p1", "p-value for non-zero effect of Factor I bipolar"],
214 ["LogL1", "Log likelihood when there is no effect of Factor I bipolar"],
215 ["λ2", "Importance for Factor II secondary structure"],
216 ["p2", "p-value for non-zero effect of Factor II secondary structure"],
217 ["LogL2", "Log likelihood when there is no effect of Factor II secondary structure"],
218 ["λ3", "Importance for Factor III volume"],
219 ["p3", "p-value for non-zero effect of Factor III volume"],
220 ["LogL3", "Log likelihood when there is no effect of Factor III volume"],
221 ["λ4", "Importance for Factor IV composition"],
222 ["p4", "p-value for non-zero effect of Factor IV composition"],
223 ["LogL4", "Log likelihood when there is no effect of Factor IV composition"],
224 ["λ5", "Importance for Factor V charge"],
225 ["p5", "p-value for non-zero effect of Factor V charge"],
226 ["LogL5", "Log likelihood when there is no effect of Factor V charge"]
227 ]
228 },
229 "analysis":{
230 "authors":"Sergei L. Kosakovsky Pond",
231 "citation":"TBD",
232 "contact":"spond@temple.edu",
233 "info":"PRIME (PRoperty Informed Model of Evolution). Given a set of N amino-acid properties,\n fit a site-level model where non-synonymous rates depend on how much a non-synonymous substitution changes the \n properties of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )- lambda_2 * diff_2 (X,Y) -...).\n When lambda_k > 0, changes in property k are disfavored and when lambda_k < 0 -- they are promoted.\n At each site, N tests are performed\n A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ",
234 "requirements":"in-frame codon alignment and a phylogenetic tree",
235 "version":"0.0.1"
236 },
237 "branch attributes":{
238 "0":{
239 "Node20":{
240 "Global MG94xREV":0.001634412628363601,
241 "Nucleotide GTR":0.001684521619549293
242 },
243 "Node38":{
244 "Global MG94xREV":0.001735516181127408,
245 "Nucleotide GTR":0.00168484920326581
246 },
247 "Node4":{
248 "Global MG94xREV":0.001634082125054255,
249 "Nucleotide GTR":0.001683801387489096
250 },
251 "REFERENCE":{
252 "Global MG94xREV":0,
253 "Nucleotide GTR":0,
254 "original name":"REFERENCE"
255 },
256 "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{
257 "Global MG94xREV":0,
258 "Nucleotide GTR":0,
259 "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021"
260 },
261 "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{
262 "Global MG94xREV":0.001732287226413535,
263 "Nucleotide GTR":0.001682745450340891,
264 "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021"
265 },
266 "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{
267 "Global MG94xREV":0,
268 "Nucleotide GTR":0,
269 "original name":"epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021"
270 },
271 "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{
272 "Global MG94xREV":0.001731614558297581,
273 "Nucleotide GTR":0.00168274558227101,
274 "original name":"epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021"
275 },
276 "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":{
277 "Global MG94xREV":0.001735723689760284,
278 "Nucleotide GTR":0.001684401404203384,
279 "original name":"epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021"
280 },
281 "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{
282 "Global MG94xREV":0.001732400224923104,
283 "Nucleotide GTR":0.00168406792173386,
284 "original name":"epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021"
285 },
286 "epi_isl_1543980_hCoV_19_Singapore_490_2021":{
287 "Global MG94xREV":0.001734572372218793,
288 "Nucleotide GTR":0.001684975469042935,
289 "original name":"epi_isl_1543980/hCoV-19/Singapore/490/2021"
290 },
291 "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":{
292 "Global MG94xREV":0.001735567212797747,
293 "Nucleotide GTR":0.001684401583391051,
294 "original name":"epi_isl_1544068/hCoV-19/India/MH-NCCS-RT231527/2021"
295 },
296 "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":{
297 "Global MG94xREV":0.001732287290600434,
298 "Nucleotide GTR":0.001682745512695379,
299 "original name":"epi_isl_1573247/hCoV-19/Germany/un-RKI-I-068985/2021"
300 },
301 "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":{
302 "Global MG94xREV":0,
303 "Nucleotide GTR":0,
304 "original name":"epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021"
305 },
306 "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":{
307 "Global MG94xREV":0.001733756929863212,
308 "Nucleotide GTR":0.001684431017860219,
309 "original name":"epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021"
310 },
311 "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":{
312 "Global MG94xREV":0.001733765372843661,
313 "Nucleotide GTR":0.001684439221071522,
314 "original name":"epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021"
315 },
316 "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":{
317 "Global MG94xREV":0,
318 "Nucleotide GTR":0,
319 "original name":"epi_isl_1615709/hCoV-19/England/CAMC-14E792B/2021"
320 },
321 "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":{
322 "Global MG94xREV":0.001736016199323374,
323 "Nucleotide GTR":0.00168443927661716,
324 "original name":"epi_isl_1632256/hCoV-19/England/RAND-14E1D70/2021"
325 },
326 "epi_isl_1652105_hCoV_19_Singapore_561_2021":{
327 "Global MG94xREV":0.001733699172098583,
328 "Nucleotide GTR":0.001685171120971631,
329 "original name":"epi_isl_1652105/hCoV-19/Singapore/561/2021"
330 },
331 "epi_isl_1652118_hCoV_19_Singapore_575_2021":{
332 "Global MG94xREV":0.001733317353440973,
333 "Nucleotide GTR":0.001684401899924961,
334 "original name":"epi_isl_1652118/hCoV-19/Singapore/575/2021"
335 },
336 "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":{
337 "Global MG94xREV":0.01050948249155059,
338 "Nucleotide GTR":0.01020457779555702,
339 "original name":"gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human"
340 },
341 "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":{
342 "Global MG94xREV":0.02683667579915389,
343 "Nucleotide GTR":0.02592331511084145,
344 "original name":"gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human"
345 },
346 "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":{
347 "Global MG94xREV":0.005257318382497578,
348 "Nucleotide GTR":0.005093980037543817,
349 "original name":"gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human"
350 },
351 "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":{
352 "Global MG94xREV":0.003479916215882181,
353 "Nucleotide GTR":0.003379296026417724,
354 "original name":"gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human"
355 },
356 "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":{
357 "Global MG94xREV":0.003464849064677958,
358 "Nucleotide GTR":0.003372774424630234,
359 "original name":"gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human"
360 },
361 "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":{
362 "Global MG94xREV":0.00347332934630856,
363 "Nucleotide GTR":0.003374190595560375,
364 "original name":"gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human"
365 },
366 "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":{
367 "Global MG94xREV":0.00521423750425419,
368 "Nucleotide GTR":0.00505933790460295,
369 "original name":"gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human"
370 },
371 "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":{
372 "Global MG94xREV":0.003464011560303172,
373 "Nucleotide GTR":0.003373764235314068,
374 "original name":"gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human"
375 },
376 "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":{
377 "Global MG94xREV":0.005236219925335357,
378 "Nucleotide GTR":0.005068409188375663,
379 "original name":"gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human"
380 },
381 "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":{
382 "Global MG94xREV":0.003464842721718857,
383 "Nucleotide GTR":0.003372774424770855,
384 "original name":"gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human"
385 },
386 "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":{
387 "Global MG94xREV":0.001735902729272567,
388 "Nucleotide GTR":0.001686266012390882,
389 "original name":"gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human"
390 },
391 "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":{
392 "Global MG94xREV":0.003480097445990996,
393 "Nucleotide GTR":0.003374436490976879,
394 "original name":"gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human"
395 },
396 "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":{
397 "Global MG94xREV":0.003472571047451632,
398 "Nucleotide GTR":0.003376034743011948,
399 "original name":"gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human"
400 },
401 "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":{
402 "Global MG94xREV":0.003474988463696198,
403 "Nucleotide GTR":0.003374190741831846,
404 "original name":"gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human"
405 },
406 "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":{
407 "Global MG94xREV":0.003471294880575992,
408 "Nucleotide GTR":0.003376937492543959,
409 "original name":"gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human"
410 }
411 },
412 "attributes":{
413 "Global MG94xREV":{
414 "attribute type":"branch length",
415 "display order":1
416 },
417 "Nucleotide GTR":{
418 "attribute type":"branch length",
419 "display order":0
420 },
421 "original name":{
422 "attribute type":"node label",
423 "display order":-1
424 }
425 }
426 },
427 "data partitions":{
428 "0":{
429 "coverage": [
430 [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]
431 ],
432 "name":"prime.filter.default"
433 }
434 },
435 "fits":{
436 "Global MG94xREV":{
437 "AIC-c":2512.962001128159,
438 "Equilibrium frequencies": [
439 [0.03825952761243274],
440 [0.01370948533169502],
441 [0.0238326285579188],
442 [0.05169206288834598],
443 [0.02910782227384961],
444 [0.01043016700423795],
445 [0.01813184740308045],
446 [0.03932728586627101],
447 [0.01035067712195123],
448 [0.003708944282165923],
449 [0.006447644771501305],
450 [0.01398469573761802],
451 [0.0283653688047424],
452 [0.01016412464618009],
453 [0.01766935821790241],
454 [0.03832416445281453],
455 [0.01521889661505549],
456 [0.005453366858635389],
457 [0.009480156518454269],
458 [0.02056209812326697],
459 [0.01157852606970437],
460 [0.004148917752546374],
461 [0.007212496554133422],
462 [0.01564363009947405],
463 [0.00411729822204095],
464 [0.001475345962268018],
465 [0.002564747797779777],
466 [0.005562840210150803],
467 [0.01128319250724396],
468 [0.004043091272315801],
469 [0.007028527343480687],
470 [0.01524460789411934],
471 [0.03592403244011121],
472 [0.01287261047188149],
473 [0.02237780168434643],
474 [0.04853659885475865],
475 [0.02733097915424774],
476 [0.009793473186905268],
477 [0.01702501611901085],
478 [0.03692661100139533],
479 [0.009718835644621534],
480 [0.003482537371104292],
481 [0.0060540580187001],
482 [0.01313102107355921],
483 [0.02663384763763138],
484 [0.009543670983435077],
485 [0.01659075888876379],
486 [0.0359847236220365],
487 [0.00848480075962617],
488 [0.03199221880690793],
489 [0.01801483181642438],
490 [0.006455230577911434],
491 [0.01122180073845716],
492 [0.02433965804833868],
493 [0.002295465694104339],
494 [0.003990447484454917],
495 [0.008655128485630147],
496 [0.01755532734880559],
497 [0.00629057695692368],
498 [0.01093556617204019],
499 [0.02371882618448924]
500 ],
501 "Log Likelihood":-1205.058976375664,
502 "Rate Distributions":{
503 "non-synonymous/synonymous rate ratio for *background*": [
504 [0.4929148115989916, 1]
505 ],
506 "non-synonymous/synonymous rate ratio for *test*": [
507 [24.3195468932995, 1]
508 ]
509 },
510 "display order":1,
511 "estimated parameters":51
512 },
513 "Nucleotide GTR":{
514 "AIC-c":2633.0046471406,
515 "Equilibrium frequencies": [
516 [0.3251262626262627],
517 [0.1799242424242424],
518 [0.2026515151515151],
519 [0.2922979797979798]
520 ],
521 "Log Likelihood":-1247.247280799152,
522 "Rate Distributions":{
523 "Substitution rate from nucleotide A to nucleotide C":0,
524 "Substitution rate from nucleotide A to nucleotide G":1,
525 "Substitution rate from nucleotide A to nucleotide T":0.3101631549852981,
526 "Substitution rate from nucleotide C to nucleotide G":1.129990583516242,
527 "Substitution rate from nucleotide C to nucleotide T":2.723444388603395,
528 "Substitution rate from nucleotide G to nucleotide T":1.720896006888861
529 },
530 "display order":0,
531 "estimated parameters":69
532 }
533 },
534 "input":{
535 "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas",
536 "number of sequences":32,
537 "number of sites":198,
538 "partition count":1,
539 "trees":{
540 "0":"(REFERENCE,(gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human,epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021)Node20,gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human,epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021,(epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021,gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human)Node4,epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021,gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human,gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human,epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021,gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human,(gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human,gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human,epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021)Node38,epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021,gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human,epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021,gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human,epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021,epi_isl_1543980_hCoV_19_Singapore_490_2021,epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021,gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human,epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021,gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human,gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human,epi_isl_1652118_hCoV_19_Singapore_575_2021,epi_isl_1652105_hCoV_19_Singapore_561_2021,gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human,gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human,epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)"
541 }
542 },
543 "tested":{
544 "0":{
545 "Node20":"test",
546 "Node38":"background",
547 "Node4":"test",
548 "REFERENCE":"background",
549 "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"background",
550 "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"background",
551 "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"background",
552 "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"background",
553 "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"background",
554 "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"background",
555 "epi_isl_1543980_hCoV_19_Singapore_490_2021":"background",
556 "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"background",
557 "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"background",
558 "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"background",
559 "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"background",
560 "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"background",
561 "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"background",
562 "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"background",
563 "epi_isl_1652105_hCoV_19_Singapore_561_2021":"background",
564 "epi_isl_1652118_hCoV_19_Singapore_575_2021":"background",
565 "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"background",
566 "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"background",
567 "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"background",
568 "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"background",
569 "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"background",
570 "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"background",
571 "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"background",
572 "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":"background",
573 "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":"background",
574 "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"background",
575 "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"background",
576 "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"background",
577 "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"background",
578 "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"background",
579 "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"background"
580 }
581 },
582 "timers":{
583 "Model fitting":{
584 "order":1,
585 "timer":5
586 },
587 "PRIME analysis":{
588 "order":2,
589 "timer":19
590 },
591 "Total time":{
592 "order":0,
593 "timer":25
594 }
595 }
596 }