Mercurial > repos > iuc > hyphy_absrel

comparison test-data/summary/nsp8.MEME.json @ 27:8633ea985719 draft

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 00684bab4c9e740cfa6a39abc444380e6818fd97"
author iuc
date Wed, 09 Jun 2021 07:04:45 +0000
parents
children
comparison
equal deleted inserted replaced
26:5f2ca10db92a 27:8633ea985719
1 {
2 "MLE":{
3 "content":{
4 "0": [
5 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
6 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
7 [3.180864197338322, 2.543979863949704, 1, 4.771296296007484, 0, 0, 0.6666666666666666, 0, 0, -9.280586212023099, -9.280586212023099],
8 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
9 [0.0002152055713864022, 5.380139284660055e-05, 1, 0.5537159057721711, 0, 0, 0.6666666666666666, 0, 0, -9.653547986238197, -9.653323462942367],
10 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
11 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
12 [3.192432742671397, 2.614421539287398, 1, 4.788649114007091, 0, 0, 0.6666666666666666, 0, 0, -9.282601941350496, -9.282601941350496],
13 [0, 0, 1, 1.464518485321612, 0, 0, 0.6666666666666666, 0, 0, -10.62393719963694, -10.62320682078165],
14 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
15 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
16 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
17 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
18 [6.613018745603487, 0.9469109242998108, 1, 9.919528118405228, 0, 0, 0.6666666666666666, 0, 0, -9.287223836219399, -9.287223836219399],
19 [0, 0, 1, 0.4712554259319698, 0, 0, 0.6666666666666666, 0, 0, -16.66043872325964, -16.66020536350117],
20 [6.613018745603487, 0.9469109242998108, 1, 9.919528118405228, 0, 0, 0.6666666666666666, 0, 0, -9.287223836219399, -9.287223836219399],
21 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
22 [6.184493076847391, 0.9840443673414764, 1, 14.36467313781675, 0, 0, 0.6666666666666666, 0, 0, -8.397276622473779, -8.39727424153126],
23 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
24 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
25 [0, 0, 1, 1.640491119619624, 0, 0, 0.6666666666666666, 0, 0, -9.354308226158436, -9.353594494276042],
26 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
27 [0, 0, 1, 0.501598063392769, 0, 0, 0.6666666666666666, 0, 0, -8.522470337679948, -8.522266927380841],
28 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
29 [6.183281758268945, 0.7526223661612934, 1, 20.13077820217984, 0, 0, 0.6666666666666666, 0, 0, -8.672432133180507, -8.672432133180507],
30 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
31 [0, 0, 1, 0.5512309724476928, 0, 0, 0.6666666666666666, 0, 0, -9.420342677733165, -9.420102843444187],
32 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
33 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
34 [20.55396794793096, 0, 1, 30.83095192189643, 0, 0, 0.6666666666666666, 0, 0, -15.39183141266653, -15.39183141266653],
35 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
36 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
37 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
38 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
39 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
40 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
41 [11.94069241655939, 1.294861562443251, 1e-08, 3408.05771887139, 0.9999999899999999, 8.386841845077999, 0.006668512759224421, 1, 0, -8.544833462621876, -8.54400349923981],
42 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
43 [0, 0, 1, 2.667290430871263, 0, 0, 0.6666666666666666, 0, 0, -6.676160314084659, -6.675420533850337],
44 [15.28765906802091, 0.5510526648388843, 1, 0.9197801610675972, 0, 0, 0.6666666666666666, 0, 0, -8.143971341837663, -8.143971341837663],
45 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
46 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
47 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
48 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
49 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
50 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
51 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
52 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
53 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
54 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
55 [0, 0, 0.7340000026600002, 1.664161295283797, 0.2659999973399998, -0.0004958679801596588, 0.6666666666666666, 0, 0, -10.6790535370286, -10.67690847747361],
56 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
57 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
58 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
59 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
60 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
61 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
62 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
63 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
64 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
65 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
66 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
67 [6.183281758268945, 0.7526223661612934, 1, 20.13077820217984, 0, 0, 0.6666666666666666, 0, 0, -8.674637993079521, -8.674637993079521],
68 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
69 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
70 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
71 [0.5786937196373596, 0.1446734299093399, 1, 1.004916925444439, 0, 0, 0.6666666666666666, 0, 0, -11.32696268611343, -11.32652486831468],
72 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
73 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
74 [1.129710780017527, 0.9171597633136092, 1, 2.114127269504442, 0, 0, 0.6666666666666666, 0, 0, -10.68005440963121, -10.68005440963121],
75 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
76 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
77 [15.27508756397395, 1.103507670905478, 1, 0.9197194398204643, 0, 0, 0.6666666666666666, 0, 0, -9.066446358261896, -9.066446358261896],
78 [0, 0, 1, 0.3002103330212254, 0, 0, 0.6666666666666666, 0, 0, -8.073134726926657, -8.073004107705682],
79 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
80 [0, 0, 1, 1.507974392107734, 0, 0, 0.6666666666666666, 0, 0, -9.638686021272513, -9.637974091034566],
81 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
82 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
83 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
84 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
85 [0, 0, 1, 1.266997878275073, 0, 0, 0.6666666666666666, 0, 0, -13.76080995690204, -13.76025871434175],
86 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
87 [0, 0, 1, 1.358147735140135, 0, 0, 0.6666666666666666, 0, 0, -8.928062239323241, -8.92741105036051],
88 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
89 [0.4526866128384942, 0.3718393063689521, 0.6988180030118201, 1.017497224439835, 0.3011819969881799, -0.01519839475007956, 0.6666666666666666, 0, 0, -12.69173819940283, -12.68265617111986],
90 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
91 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
92 [0, 0, 0.8, 0, 0.2, 0, 0.6666666666666666, 0, 0, -9.358363158677459, -9.358363158677459],
93 [0, 0, 1, 1.938326252496763, 0, 0, 0.6666666666666666, 0, 0, -8.509867904824112, -8.509404247968943],
94 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
95 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
96 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
97 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
98 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
99 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
100 [0, 0, 0.7490150025098501, 0.1049473027672059, 0.2509849974901499, -2.200854539680108e-05, 0.6666666666666666, 0, 0, -8.464242350192716, -8.464192449728422],
101 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
102 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
103 [20.86865842045917, 0.600388814460612, 1, 31.30298763068872, 0, 0, 0.6666666666666666, 0, 0, -7.336832893614085, -7.336832893614085],
104 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
105 [20.86865842045917, 0.600388814460612, 1, 31.30298763068872, 0, 0, 0.6666666666666666, 0, 0, -7.338795266882312, -7.338795266882312],
106 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
107 [3.203873682906836, 1.501479279648967, 1, 4.805810524360257, 0, 0, 0.6666666666666666, 0, 0, -10.86406980762116, -10.86406980762116],
108 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
109 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
110 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
111 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
112 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
113 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
114 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
115 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
116 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
117 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
118 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
119 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
120 [3.246494618001559, 2.634772693661996, 1, 4.869741927002336, 0, 0, 0.6666666666666666, 0, 0, -10.8385140535094, -10.8385140535094],
121 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
122 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
123 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
124 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
125 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
126 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
127 [0, 0, 1, 1.789076154151788, 0, 0, 0.6666666666666666, 0, 0, -9.2047661806742, -9.204336423724397],
128 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
129 [0, 0, 0.7709850022901499, 0.08094025545997562, 0.2290149977098501, -1.61302205974323e-05, 0.6666666666666666, 0, 0, -7.421831643595838, -7.421770618566589],
130 [0, 0, 1, 1.929658045798704, 0, 0, 0.6666666666666666, 0, 0, -8.458626059199007, -8.457949370508054],
131 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
132 [5.199393870663767, 1.499789961783057, 1, 14.71138673404418, 0, 0, 0.6666666666666666, 0, 0, -10.02737457526561, -10.02737457526561],
133 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
134 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
135 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
136 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
137 [0, 0, 1e-08, 2726.483703129013, 0.9999999899999999, 10.37890154001262, 0.002426582108613462, 1, 0, -7.246578528906719, -7.246538510993981],
138 [0, 0, 1, 3.859443894515683, 0, 0, 0.6666666666666666, 0, 0, -7.912077519287077, -7.911090684261904],
139 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
140 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
141 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
142 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
143 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
144 [0, 0, 1, 1.958052817869167, 0, 0, 0.6666666666666666, 0, 0, -9.382033288803258, -9.381643179903982],
145 [3.862010608338021, 2.491129766976171, 1, 5.793015912507029, 0, 0, 0.6666666666666666, 0, 0, -8.329908611803257, -8.329908611803257],
146 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
147 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
148 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
149 [0, 0, 1, 1.437221691867563, 0, 0, 0.6666666666666666, 0, 0, -8.107305627397892, -8.106957574811677],
150 [0, 0, 1, 1.789076154151788, 0, 0, 0.6666666666666666, 0, 0, -9.204761319552047, -9.204331562602245],
151 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
152 [0, 0, 1, 0.9806683950122447, 0, 0, 0.6666666666666666, 0, 0, -7.810274303056883, -7.810036168495238],
153 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
154 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
155 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
156 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
157 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
158 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
159 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
160 [4.06016401094355, 0.7757847450990135, 1, 9.984323985462302, 0, 0, 0.6666666666666666, 0, 0, -8.593437290682184, -8.593437290682184],
161 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
162 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
163 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
164 [14.32982957244073, 1.242379135936381, 1, 21.49474435866112, 0, 0, 0.6666666666666666, 0, 0, -9.290422613892463, -9.290422613892463],
165 [0, 0, 1, 0.1355031069705359, 0, 0, 0.6666666666666666, 0, 0, -6.700513535353661, -6.70046128134527],
166 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
167 [20.26324400145215, 0, 1, 0.9382618221089256, 0, 0, 0.6666666666666666, 0, 0, -11.00989212007257, -11.00989212007257],
168 [0, 0, 1, 1.603811733757937, 0, 0, 0.6666666666666666, 0, 0, -7.988973026764041, -7.988145241715093],
169 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
170 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
171 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
172 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
173 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
174 [0, 0, 1, 0.008996126907272754, 0, 0, 0.6666666666666666, 0, 0, -14.79406886244202, -14.79406421908668],
175 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
176 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
177 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
178 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
179 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
180 [21.00519221068461, 1.915676726331522, 1, 0.940312384060174, 0, 0, 0.6666666666666666, 0, 0, -7.275925155507314, -7.275925155507314],
181 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
182 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
183 [21.00519221068461, 1.915676726331522, 1, 0.940312384060174, 0, 0, 0.6666666666666666, 0, 0, -7.275923445834203, -7.275923445834203],
184 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
185 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
186 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
187 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
188 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
189 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
190 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
191 [14.23574537614087, 0, 1, 21.35361806421129, 0, 0, 0.6666666666666666, 0, 0, -14.16530148856323, -14.16530148856323],
192 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
193 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
194 [0, 0, 1, 2.82801162274558, 0, 0, 0.6666666666666666, 0, 0, -9.192071259452563, -9.190269071584945],
195 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
196 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
197 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
198 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
199 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
200 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
201 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
202 [0.0001047939488656373, 2.619848721640933e-05, 1, 1.231388513343972, 0, 0, 0.6666666666666666, 0, 0, -13.77239892007799, -13.77191643637779]
203 ]
204 },
205 "headers": [
206 ["alpha;", "Synonymous substitution rate at a site"],
207 ["&beta;<sup>-</sup>", "Non-synonymous substitution rate at a site for the negative/neutral evolution component"],
208 ["p<sup>-</sup>", "Mixture distribution weight allocated to &beta;<sup>-</sup>; loosely -- the proportion of the tree evolving neutrally or under negative selection"],
209 ["&beta;<sup>+</sup>", "Non-synonymous substitution rate at a site for the positive/neutral evolution component"],
210 ["p<sup>+</sup>", "Mixture distribution weight allocated to &beta;<sup>+</sup>; loosely -- the proportion of the tree evolving neutrally or under positive selection"],
211 ["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p<sup>+</sup> &gt; 0 <emph>and<emph> &beta;<sup>+</sup> &gt; &alpha;"],
212 ["p-value", "Asymptotic p-value for episodic diversification, i.e., p<sup>+</sup> &gt; 0 <emph>and<emph> &beta;<sup>+</sup> &gt; &alpha;"],
213 ["# branches under selection", "The (very approximate and rough) estimate of how many branches may have been under selection at this site, i.e., had an empirical Bayes factor of 100 or more for the &beta;<sup>+</sup> rate"],
214 ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"],
215 ["MEME LogL", "Site Log-likelihood under the MEME model"],
216 ["FEL LogL", "Site Log-likelihood under the FEL model"]
217 ]
218 },
219 "analysis":{
220 "authors":"Sergei L. Kosakovsky Pond, Steven Weaver",
221 "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.",
222 "contact":"spond@temple.edu",
223 "info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (&alpha;) and a two-category mixture of non-synonymous\n (&beta;-, with proportion p-, and &beta;+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if &beta;+ > &alpha; at a site.\n The estimates aggregate information over a proportion of branches at a site,\n so the signal is derived from\n episodic diversification, which is a combination of strength of selection [effect size] and\n the proportion of the tree affected. 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 ",
224 "requirements":"in-frame codon alignment and a phylogenetic tree",
225 "version":"2.1.2"
226 },
227 "branch attributes":{
228 "0":{
229 "Node20":{
230 "EBF site 101 (partition 1)":1,
231 "EBF site 103 (partition 1)":1,
232 "EBF site 116 (partition 1)":1,
233 "EBF site 123 (partition 1)":1,
234 "EBF site 125 (partition 1)":0.9999823899944797,
235 "EBF site 126 (partition 1)":1,
236 "EBF site 128 (partition 1)":1,
237 "EBF site 133 (partition 1)":0.5654898147900533,
238 "EBF site 134 (partition 1)":1,
239 "EBF site 14 (partition 1)":1,
240 "EBF site 140 (partition 1)":1,
241 "EBF site 141 (partition 1)":1,
242 "EBF site 145 (partition 1)":1,
243 "EBF site 146 (partition 1)":1,
244 "EBF site 148 (partition 1)":1,
245 "EBF site 15 (partition 1)":1,
246 "EBF site 156 (partition 1)":1,
247 "EBF site 16 (partition 1)":1,
248 "EBF site 160 (partition 1)":1,
249 "EBF site 161 (partition 1)":1,
250 "EBF site 163 (partition 1)":1,
251 "EBF site 164 (partition 1)":1,
252 "EBF site 170 (partition 1)":1,
253 "EBF site 176 (partition 1)":1,
254 "EBF site 179 (partition 1)":1,
255 "EBF site 18 (partition 1)":1,
256 "EBF site 187 (partition 1)":1,
257 "EBF site 190 (partition 1)":1,
258 "EBF site 198 (partition 1)":1,
259 "EBF site 21 (partition 1)":1,
260 "EBF site 23 (partition 1)":1,
261 "EBF site 25 (partition 1)":1,
262 "EBF site 27 (partition 1)":1,
263 "EBF site 3 (partition 1)":1,
264 "EBF site 30 (partition 1)":1,
265 "EBF site 37 (partition 1)":1616.162948531769,
266 "EBF site 39 (partition 1)":1,
267 "EBF site 40 (partition 1)":1,
268 "EBF site 5 (partition 1)":1,
269 "EBF site 51 (partition 1)":0.9995339403671608,
270 "EBF site 63 (partition 1)":1,
271 "EBF site 67 (partition 1)":1,
272 "EBF site 70 (partition 1)":1,
273 "EBF site 73 (partition 1)":1,
274 "EBF site 74 (partition 1)":1,
275 "EBF site 76 (partition 1)":1,
276 "EBF site 8 (partition 1)":1,
277 "EBF site 81 (partition 1)":1,
278 "EBF site 83 (partition 1)":1,
279 "EBF site 85 (partition 1)":0.9998333727208876,
280 "EBF site 88 (partition 1)":1,
281 "EBF site 89 (partition 1)":1,
282 "EBF site 9 (partition 1)":1,
283 "EBF site 96 (partition 1)":0.9999780756681181,
284 "EBF site 99 (partition 1)":1,
285 "Global MG94xREV":0.001634413111541721,
286 "Nucleotide GTR":0.001684521619549293
287 },
288 "Node38":{
289 "Global MG94xREV":0.001735516182878667,
290 "Nucleotide GTR":0.00168484920326581
291 },
292 "Node4":{
293 "EBF site 101 (partition 1)":1,
294 "EBF site 103 (partition 1)":1,
295 "EBF site 116 (partition 1)":1,
296 "EBF site 123 (partition 1)":1,
297 "EBF site 125 (partition 1)":0.9999823935606595,
298 "EBF site 126 (partition 1)":1,
299 "EBF site 128 (partition 1)":1,
300 "EBF site 133 (partition 1)":1e+26,
301 "EBF site 134 (partition 1)":1,
302 "EBF site 14 (partition 1)":1,
303 "EBF site 140 (partition 1)":1,
304 "EBF site 141 (partition 1)":1,
305 "EBF site 145 (partition 1)":1,
306 "EBF site 146 (partition 1)":1,
307 "EBF site 148 (partition 1)":1,
308 "EBF site 15 (partition 1)":1,
309 "EBF site 156 (partition 1)":1,
310 "EBF site 16 (partition 1)":1,
311 "EBF site 160 (partition 1)":1,
312 "EBF site 161 (partition 1)":1,
313 "EBF site 163 (partition 1)":1,
314 "EBF site 164 (partition 1)":1,
315 "EBF site 170 (partition 1)":1,
316 "EBF site 176 (partition 1)":1,
317 "EBF site 179 (partition 1)":1,
318 "EBF site 18 (partition 1)":1,
319 "EBF site 187 (partition 1)":1,
320 "EBF site 190 (partition 1)":1,
321 "EBF site 198 (partition 1)":1,
322 "EBF site 21 (partition 1)":1,
323 "EBF site 23 (partition 1)":1,
324 "EBF site 25 (partition 1)":1,
325 "EBF site 27 (partition 1)":1,
326 "EBF site 3 (partition 1)":1,
327 "EBF site 30 (partition 1)":1,
328 "EBF site 37 (partition 1)":0.5725438663972433,
329 "EBF site 39 (partition 1)":1,
330 "EBF site 40 (partition 1)":1,
331 "EBF site 5 (partition 1)":1,
332 "EBF site 51 (partition 1)":0.9995340347254161,
333 "EBF site 63 (partition 1)":1,
334 "EBF site 67 (partition 1)":1,
335 "EBF site 70 (partition 1)":1,
336 "EBF site 73 (partition 1)":1,
337 "EBF site 74 (partition 1)":1,
338 "EBF site 76 (partition 1)":1,
339 "EBF site 8 (partition 1)":1,
340 "EBF site 81 (partition 1)":1,
341 "EBF site 83 (partition 1)":1,
342 "EBF site 85 (partition 1)":0.9998334064611279,
343 "EBF site 88 (partition 1)":1,
344 "EBF site 89 (partition 1)":1,
345 "EBF site 9 (partition 1)":1,
346 "EBF site 96 (partition 1)":0.9999780801079843,
347 "EBF site 99 (partition 1)":1,
348 "Global MG94xREV":0.001634082124753167,
349 "Nucleotide GTR":0.001683801387489096
350 },
351 "REFERENCE":{
352 "Global MG94xREV":0,
353 "Nucleotide GTR":0,
354 "original name":"REFERENCE"
355 },
356 "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{
357 "Global MG94xREV":0,
358 "Nucleotide GTR":0,
359 "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021"
360 },
361 "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{
362 "Global MG94xREV":0.001732287228161539,
363 "Nucleotide GTR":0.001682745450340891,
364 "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021"
365 },
366 "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{
367 "Global MG94xREV":0,
368 "Nucleotide GTR":0,
369 "original name":"epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021"
370 },
371 "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{
372 "Global MG94xREV":0.001731614560044905,
373 "Nucleotide GTR":0.00168274558227101,
374 "original name":"epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021"
375 },
376 "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":{
377 "Global MG94xREV":0.001735723691511758,
378 "Nucleotide GTR":0.001684401404203384,
379 "original name":"epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021"
380 },
381 "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{
382 "Global MG94xREV":0.001732400226671219,
383 "Nucleotide GTR":0.00168406792173386,
384 "original name":"epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021"
385 },
386 "epi_isl_1543980_hCoV_19_Singapore_490_2021":{
387 "Global MG94xREV":0.001734572373969102,
388 "Nucleotide GTR":0.001684975469042935,
389 "original name":"epi_isl_1543980/hCoV-19/Singapore/490/2021"
390 },
391 "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":{
392 "Global MG94xREV":0.001735567214549057,
393 "Nucleotide GTR":0.001684401583391051,
394 "original name":"epi_isl_1544068/hCoV-19/India/MH-NCCS-RT231527/2021"
395 },
396 "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":{
397 "Global MG94xREV":0.001732287292348436,
398 "Nucleotide GTR":0.001682745512695379,
399 "original name":"epi_isl_1573247/hCoV-19/Germany/un-RKI-I-068985/2021"
400 },
401 "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":{
402 "Global MG94xREV":0,
403 "Nucleotide GTR":0,
404 "original name":"epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021"
405 },
406 "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":{
407 "Global MG94xREV":0.001733756931612698,
408 "Nucleotide GTR":0.001684431017860219,
409 "original name":"epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021"
410 },
411 "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":{
412 "Global MG94xREV":0.001733765374593157,
413 "Nucleotide GTR":0.001684439221071522,
414 "original name":"epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021"
415 },
416 "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":{
417 "Global MG94xREV":0,
418 "Nucleotide GTR":0,
419 "original name":"epi_isl_1615709/hCoV-19/England/CAMC-14E792B/2021"
420 },
421 "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":{
422 "Global MG94xREV":0.001736016201075139,
423 "Nucleotide GTR":0.00168443927661716,
424 "original name":"epi_isl_1632256/hCoV-19/England/RAND-14E1D70/2021"
425 },
426 "epi_isl_1652105_hCoV_19_Singapore_561_2021":{
427 "Global MG94xREV":0.001733699173848011,
428 "Nucleotide GTR":0.001685171120971631,
429 "original name":"epi_isl_1652105/hCoV-19/Singapore/561/2021"
430 },
431 "epi_isl_1652118_hCoV_19_Singapore_575_2021":{
432 "Global MG94xREV":0.001733317355190017,
433 "Nucleotide GTR":0.001684401899924961,
434 "original name":"epi_isl_1652118/hCoV-19/Singapore/575/2021"
435 },
436 "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":{
437 "Global MG94xREV":0.01050948250215542,
438 "Nucleotide GTR":0.01020457779555702,
439 "original name":"gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human"
440 },
441 "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":{
442 "Global MG94xREV":0.02683667582570331,
443 "Nucleotide GTR":0.02592331511084145,
444 "original name":"gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human"
445 },
446 "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":{
447 "Global MG94xREV":0.005257318387802578,
448 "Nucleotide GTR":0.005093980037543817,
449 "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"
450 },
451 "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":{
452 "Global MG94xREV":0.003479916219393658,
453 "Nucleotide GTR":0.003379296026417724,
454 "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"
455 },
456 "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":{
457 "Global MG94xREV":0.003464849068174243,
458 "Nucleotide GTR":0.003372774424630234,
459 "original name":"gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human"
460 },
461 "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":{
462 "Global MG94xREV":0.003473329349813396,
463 "Nucleotide GTR":0.003374190595560375,
464 "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"
465 },
466 "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":{
467 "Global MG94xREV":0.00521423750951572,
468 "Nucleotide GTR":0.00505933790460295,
469 "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"
470 },
471 "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":{
472 "Global MG94xREV":0.003464011563798612,
473 "Nucleotide GTR":0.003373764235314068,
474 "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"
475 },
476 "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":{
477 "Global MG94xREV":0.005236219930619085,
478 "Nucleotide GTR":0.005068409188375663,
479 "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"
480 },
481 "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":{
482 "Global MG94xREV":0.003464842725215135,
483 "Nucleotide GTR":0.003372774424770855,
484 "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"
485 },
486 "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":{
487 "Global MG94xREV":0.001735902731024219,
488 "Nucleotide GTR":0.001686266012390882,
489 "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"
490 },
491 "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":{
492 "Global MG94xREV":0.00348009744950267,
493 "Nucleotide GTR":0.003374436490976879,
494 "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"
495 },
496 "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":{
497 "Global MG94xREV":0.003472571050955705,
498 "Nucleotide GTR":0.003376034743011948,
499 "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"
500 },
501 "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":{
502 "Global MG94xREV":0.003474988467202712,
503 "Nucleotide GTR":0.003374190741831846,
504 "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"
505 },
506 "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":{
507 "Global MG94xREV":0.003471294884078775,
508 "Nucleotide GTR":0.003376937492543959,
509 "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"
510 }
511 },
512 "attributes":{
513 "EBF site 101 (partition 1)":{
514 "attribute type":"branch label",
515 "display order":200
516 },
517 "EBF site 103 (partition 1)":{
518 "attribute type":"branch label",
519 "display order":200
520 },
521 "EBF site 116 (partition 1)":{
522 "attribute type":"branch label",
523 "display order":200
524 },
525 "EBF site 123 (partition 1)":{
526 "attribute type":"branch label",
527 "display order":200
528 },
529 "EBF site 125 (partition 1)":{
530 "attribute type":"branch label",
531 "display order":200
532 },
533 "EBF site 126 (partition 1)":{
534 "attribute type":"branch label",
535 "display order":200
536 },
537 "EBF site 128 (partition 1)":{
538 "attribute type":"branch label",
539 "display order":200
540 },
541 "EBF site 133 (partition 1)":{
542 "attribute type":"branch label",
543 "display order":200
544 },
545 "EBF site 134 (partition 1)":{
546 "attribute type":"branch label",
547 "display order":200
548 },
549 "EBF site 14 (partition 1)":{
550 "attribute type":"branch label",
551 "display order":200
552 },
553 "EBF site 140 (partition 1)":{
554 "attribute type":"branch label",
555 "display order":200
556 },
557 "EBF site 141 (partition 1)":{
558 "attribute type":"branch label",
559 "display order":200
560 },
561 "EBF site 145 (partition 1)":{
562 "attribute type":"branch label",
563 "display order":200
564 },
565 "EBF site 146 (partition 1)":{
566 "attribute type":"branch label",
567 "display order":200
568 },
569 "EBF site 148 (partition 1)":{
570 "attribute type":"branch label",
571 "display order":200
572 },
573 "EBF site 15 (partition 1)":{
574 "attribute type":"branch label",
575 "display order":200
576 },
577 "EBF site 156 (partition 1)":{
578 "attribute type":"branch label",
579 "display order":200
580 },
581 "EBF site 16 (partition 1)":{
582 "attribute type":"branch label",
583 "display order":200
584 },
585 "EBF site 160 (partition 1)":{
586 "attribute type":"branch label",
587 "display order":200
588 },
589 "EBF site 161 (partition 1)":{
590 "attribute type":"branch label",
591 "display order":200
592 },
593 "EBF site 163 (partition 1)":{
594 "attribute type":"branch label",
595 "display order":200
596 },
597 "EBF site 164 (partition 1)":{
598 "attribute type":"branch label",
599 "display order":200
600 },
601 "EBF site 170 (partition 1)":{
602 "attribute type":"branch label",
603 "display order":200
604 },
605 "EBF site 176 (partition 1)":{
606 "attribute type":"branch label",
607 "display order":200
608 },
609 "EBF site 179 (partition 1)":{
610 "attribute type":"branch label",
611 "display order":200
612 },
613 "EBF site 18 (partition 1)":{
614 "attribute type":"branch label",
615 "display order":200
616 },
617 "EBF site 187 (partition 1)":{
618 "attribute type":"branch label",
619 "display order":200
620 },
621 "EBF site 190 (partition 1)":{
622 "attribute type":"branch label",
623 "display order":200
624 },
625 "EBF site 198 (partition 1)":{
626 "attribute type":"branch label",
627 "display order":200
628 },
629 "EBF site 21 (partition 1)":{
630 "attribute type":"branch label",
631 "display order":200
632 },
633 "EBF site 23 (partition 1)":{
634 "attribute type":"branch label",
635 "display order":200
636 },
637 "EBF site 25 (partition 1)":{
638 "attribute type":"branch label",
639 "display order":200
640 },
641 "EBF site 27 (partition 1)":{
642 "attribute type":"branch label",
643 "display order":200
644 },
645 "EBF site 3 (partition 1)":{
646 "attribute type":"branch label",
647 "display order":200
648 },
649 "EBF site 30 (partition 1)":{
650 "attribute type":"branch label",
651 "display order":200
652 },
653 "EBF site 37 (partition 1)":{
654 "attribute type":"branch label",
655 "display order":200
656 },
657 "EBF site 39 (partition 1)":{
658 "attribute type":"branch label",
659 "display order":200
660 },
661 "EBF site 40 (partition 1)":{
662 "attribute type":"branch label",
663 "display order":200
664 },
665 "EBF site 5 (partition 1)":{
666 "attribute type":"branch label",
667 "display order":200
668 },
669 "EBF site 51 (partition 1)":{
670 "attribute type":"branch label",
671 "display order":200
672 },
673 "EBF site 63 (partition 1)":{
674 "attribute type":"branch label",
675 "display order":200
676 },
677 "EBF site 67 (partition 1)":{
678 "attribute type":"branch label",
679 "display order":200
680 },
681 "EBF site 70 (partition 1)":{
682 "attribute type":"branch label",
683 "display order":200
684 },
685 "EBF site 73 (partition 1)":{
686 "attribute type":"branch label",
687 "display order":200
688 },
689 "EBF site 74 (partition 1)":{
690 "attribute type":"branch label",
691 "display order":200
692 },
693 "EBF site 76 (partition 1)":{
694 "attribute type":"branch label",
695 "display order":200
696 },
697 "EBF site 8 (partition 1)":{
698 "attribute type":"branch label",
699 "display order":200
700 },
701 "EBF site 81 (partition 1)":{
702 "attribute type":"branch label",
703 "display order":200
704 },
705 "EBF site 83 (partition 1)":{
706 "attribute type":"branch label",
707 "display order":200
708 },
709 "EBF site 85 (partition 1)":{
710 "attribute type":"branch label",
711 "display order":200
712 },
713 "EBF site 88 (partition 1)":{
714 "attribute type":"branch label",
715 "display order":200
716 },
717 "EBF site 89 (partition 1)":{
718 "attribute type":"branch label",
719 "display order":200
720 },
721 "EBF site 9 (partition 1)":{
722 "attribute type":"branch label",
723 "display order":200
724 },
725 "EBF site 96 (partition 1)":{
726 "attribute type":"branch label",
727 "display order":200
728 },
729 "EBF site 99 (partition 1)":{
730 "attribute type":"branch label",
731 "display order":200
732 },
733 "Global MG94xREV":{
734 "attribute type":"branch length",
735 "display order":1
736 },
737 "Nucleotide GTR":{
738 "attribute type":"branch length",
739 "display order":0
740 },
741 "original name":{
742 "attribute type":"node label",
743 "display order":-1
744 }
745 }
746 },
747 "data partitions":{
748 "0":{
749 "coverage": [
750 [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]
751 ],
752 "name":"meme.filter.default"
753 }
754 },
755 "fits":{
756 "Global MG94xREV":{
757 "AIC-c":2512.962001126494,
758 "Equilibrium frequencies": [
759 [0.03825952761243274],
760 [0.01370948533169502],
761 [0.0238326285579188],
762 [0.05169206288834598],
763 [0.02910782227384961],
764 [0.01043016700423795],
765 [0.01813184740308045],
766 [0.03932728586627101],
767 [0.01035067712195123],
768 [0.003708944282165923],
769 [0.006447644771501305],
770 [0.01398469573761802],
771 [0.0283653688047424],
772 [0.01016412464618009],
773 [0.01766935821790241],
774 [0.03832416445281453],
775 [0.01521889661505549],
776 [0.005453366858635389],
777 [0.009480156518454269],
778 [0.02056209812326697],
779 [0.01157852606970437],
780 [0.004148917752546374],
781 [0.007212496554133422],
782 [0.01564363009947405],
783 [0.00411729822204095],
784 [0.001475345962268018],
785 [0.002564747797779777],
786 [0.005562840210150803],
787 [0.01128319250724396],
788 [0.004043091272315801],
789 [0.007028527343480687],
790 [0.01524460789411934],
791 [0.03592403244011121],
792 [0.01287261047188149],
793 [0.02237780168434643],
794 [0.04853659885475865],
795 [0.02733097915424774],
796 [0.009793473186905268],
797 [0.01702501611901085],
798 [0.03692661100139533],
799 [0.009718835644621534],
800 [0.003482537371104292],
801 [0.0060540580187001],
802 [0.01313102107355921],
803 [0.02663384763763138],
804 [0.009543670983435077],
805 [0.01659075888876379],
806 [0.0359847236220365],
807 [0.00848480075962617],
808 [0.03199221880690793],
809 [0.01801483181642438],
810 [0.006455230577911434],
811 [0.01122180073845716],
812 [0.02433965804833868],
813 [0.002295465694104339],
814 [0.003990447484454917],
815 [0.008655128485630147],
816 [0.01755532734880559],
817 [0.00629057695692368],
818 [0.01093556617204019],
819 [0.02371882618448924]
820 ],
821 "Log Likelihood":-1205.058976374832,
822 "Rate Distributions":{
823 "non-synonymous/synonymous rate ratio for *background*": [
824 [0.4929148115209321, 1]
825 ],
826 "non-synonymous/synonymous rate ratio for *test*": [
827 [24.31954771499909, 1]
828 ]
829 },
830 "display order":1,
831 "estimated parameters":51
832 },
833 "Nucleotide GTR":{
834 "AIC-c":2633.0046471406,
835 "Equilibrium frequencies": [
836 [0.3251262626262627],
837 [0.1799242424242424],
838 [0.2026515151515151],
839 [0.2922979797979798]
840 ],
841 "Log Likelihood":-1247.247280799152,
842 "Rate Distributions":{
843 "Substitution rate from nucleotide A to nucleotide C":0,
844 "Substitution rate from nucleotide A to nucleotide G":1,
845 "Substitution rate from nucleotide A to nucleotide T":0.3101631549852981,
846 "Substitution rate from nucleotide C to nucleotide G":1.129990583516242,
847 "Substitution rate from nucleotide C to nucleotide T":2.723444388603395,
848 "Substitution rate from nucleotide G to nucleotide T":1.720896006888861
849 },
850 "display order":0,
851 "estimated parameters":69
852 }
853 },
854 "input":{
855 "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas",
856 "number of sequences":32,
857 "number of sites":198,
858 "partition count":1,
859 "trees":{
860 "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)"
861 }
862 },
863 "tested":{
864 "0":{
865 "Node20":"test",
866 "Node38":"background",
867 "Node4":"test",
868 "REFERENCE":"background",
869 "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"background",
870 "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"background",
871 "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"background",
872 "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"background",
873 "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"background",
874 "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"background",
875 "epi_isl_1543980_hCoV_19_Singapore_490_2021":"background",
876 "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"background",
877 "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"background",
878 "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"background",
879 "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"background",
880 "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"background",
881 "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"background",
882 "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"background",
883 "epi_isl_1652105_hCoV_19_Singapore_561_2021":"background",
884 "epi_isl_1652118_hCoV_19_Singapore_575_2021":"background",
885 "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"background",
886 "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"background",
887 "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",
888 "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",
889 "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"background",
890 "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",
891 "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",
892 "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",
893 "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",
894 "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",
895 "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",
896 "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",
897 "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",
898 "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",
899 "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"
900 }
901 },
902 "timers":{
903 "MEME analysis":{
904 "order":2,
905 "timer":5
906 },
907 "Model fitting":{
908 "order":1,
909 "timer":5
910 },
911 "Total time":{
912 "order":0,
913 "timer":10
914 }
915 }
916 }