Mercurial > repos > iuc > hyphy_busted

comparison test-data/meme-out1.json @ 0:edabb77ac0d4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
author iuc
date Thu, 17 Jan 2019 04:25:13 -0500
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children b678fe748dc5
comparison
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-1:000000000000 0:edabb77ac0d4
1 {
2 "analysis":{
3 "info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous\n (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if β+ > α 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 ",
4 "version":"2.0.1",
5 "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.",
6 "authors":"Sergei L. Kosakovsky Pond, Steven Weaver",
7 "contact":"spond@temple.edu",
8 "requirements":"in-frame codon alignment and a phylogenetic tree"
9 },
10 "fits":{
11 "Nucleotide GTR":{
12 "Log Likelihood":-4394.17778442101,
13 "estimated parameters":47,
14 "AIC-c":8882.482274823486,
15 "Equilibrium frequencies":[
16 [0.3460163217230355],
17 [0.1876507375623983],
18 [0.2296889898480005],
19 [0.2366439508665657]
20 ],
21 "Rate Distributions":{
22 "Substitution rate from nucleotide A to nucleotide C":0.1602243049428088,
23 "Substitution rate from nucleotide A to nucleotide G":1,
24 "Substitution rate from nucleotide A to nucleotide T":0.1350661843114337,
25 "Substitution rate from nucleotide C to nucleotide G":0.04669906431175039,
26 "Substitution rate from nucleotide C to nucleotide T":1.290725939052547,
27 "Substitution rate from nucleotide G to nucleotide T":0.1442807316736102
28 },
29 "display order":0
30 },
31 "Global MG94xREV":{
32 "Log Likelihood":-4272.739394378317,
33 "estimated parameters":54,
34 "AIC-c":8653.980859587502,
35 "Equilibrium frequencies":[
36 [0.04794212053691846],
37 [0.02918423386756777],
38 [0.03061835466109362],
39 [0.03395226455636327],
40 [0.02063374857573568],
41 [0.01256056547467788],
42 [0.01317779490778274],
43 [0.01461267216775245],
44 [0.02309512129134449],
45 [0.01405889880167917],
46 [0.01474975672164567],
47 [0.01635579860179934],
48 [0.03032452824999034],
49 [0.01845972006369387],
50 [0.01936683547765817],
51 [0.02147561255447049],
52 [0.02137643485619778],
53 [0.01301266750638816],
54 [0.01365211335015547],
55 [0.01513863724385318],
56 [0.009200176740799796],
57 [0.005600505497450756],
58 [0.005875715784779066],
59 [0.006515498921838312],
60 [0.01029765371767897],
61 [0.006268582428525358],
62 [0.0065766221888793],
63 [0.007292724214466442],
64 [0.01352110201678854],
65 [0.00823082081030041],
66 [0.008635285471781717],
67 [0.009575547089413102],
68 [0.03891475766269277],
69 [0.02368892689369449],
70 [0.02485300688252417],
71 [0.02755915117048418],
72 [0.01674847329457107],
73 [0.01019544726180969],
74 [0.01069645417478218],
75 [0.01186114818960848],
76 [0.0187463766345312],
77 [0.01141164874946168],
78 [0.01197242011780667],
79 [0.01327604894903844],
80 [0.02461450713626915],
81 [0.01498380807429274],
82 [0.01572011627491417],
83 [0.01743181671681681],
84 [0.02096427272215724],
85 [0.0243893513506083],
86 [0.01482209656025475],
87 [0.009022786801619234],
88 [0.009466168876559794],
89 [0.0104969020572672],
90 [0.01009910316608133],
91 [0.0105953757052942],
92 [0.01174906369078435],
93 [0.02178339453036125],
94 [0.01326039969204127],
95 [0.01391201915942615],
96 [0.01542684315477715]
97 ],
98 "Rate Distributions":{
99 "non-synonymous/synonymous rate ratio for *test*":[
100 [0.2936035676191999, 1]
101 ]
102 },
103 "display order":1
104 }
105 },
106 "timers":{
107 "Total time":{
108 "timer":816,
109 "order":0
110 },
111 "Model fitting":{
112 "timer":12,
113 "order":1
114 },
115 "MEME analysis":{
116 "timer":803,
117 "order":2
118 }
119 },
120 "tested":{
121 "0":{
122 "TREESPARROW_HENAN_1_2004":"test",
123 "TREESPARROW_HENAN_3_2004":"test",
124 "Node6":"test",
125 "TREESPARROW_HENAN_4_2004":"test",
126 "Node5":"test",
127 "CHICKEN_HEBEI_326_2005":"test",
128 "SWINE_ANHUI_1_2004":"test",
129 "TREESPARROW_HENAN_2_2004":"test",
130 "Node12":"test",
131 "Node10":"test",
132 "Node4":"test",
133 "CHICKEN_HONGKONG_915_97":"test",
134 "GOOSE_HONGKONG_W355_97":"test",
135 "DUCK_HONGKONG_Y283_97":"test",
136 "Node19":"test",
137 "Node17":"test",
138 "HONGKONG_1_97_98":"test",
139 "Node16":"test",
140 "HONGKONG_1_538_97":"test",
141 "Node15":"test",
142 "Node3":"test",
143 "DUCK_GUANGZHOU_20_2005":"test",
144 "GOOSE_SHANTOU_2216_2005":"test",
145 "Node26":"test",
146 "PEREGRINEFALCON_HK_D0028_2004":"test",
147 "Node25":"test",
148 "CK_HK_WF157_2003":"test",
149 "Node24":"test",
150 "Node2":"test",
151 "HUMAN_VIETNAM_CL105_2005":"test",
152 "DUCK_VIETNAM_376_2005":"test",
153 "Node33":"test",
154 "HUMAN_VIETNAM_3062_2004":"test",
155 "Node32":"test",
156 "MALLARD_VIETNAM_16_2003":"test",
157 "Node31":"test",
158 "Node1":"test",
159 "CHICKEN_CK_160_2005":"test",
160 "DUCK_VIETNAM_272_2005":"test"
161 }
162 },
163 "input":{
164 "file name":"/tmp/tmpv_gXOY/job_working_directory/002/2719/working/meme_input.fa",
165 "number of sequences":21,
166 "number of sites":566,
167 "partition count":1,
168 "trees":{
169 "0":"(((((((TREESPARROW_HENAN_1_2004:0.0111334,TREESPARROW_HENAN_3_2004:0.00619375)Node6:0.000995666,TREESPARROW_HENAN_4_2004:0.00435165)Node5:0.00226776,(CHICKEN_HEBEI_326_2005:0.0210089,(SWINE_ANHUI_1_2004:0.00770239,TREESPARROW_HENAN_2_2004:0.00906278)Node12:0.00209522)Node10:0.00388724)Node4:0.00340492,(((CHICKEN_HONGKONG_915_97:-1,(GOOSE_HONGKONG_W355_97:-1,DUCK_HONGKONG_Y283_97:0.00279842)Node19:0.00289977)Node17:0.00130638,HONGKONG_1_97_98:0.00384493)Node16:0.000182536,HONGKONG_1_538_97:-1)Node15:0.0209617)Node3:0.00313061,(((DUCK_GUANGZHOU_20_2005:0.00629939,GOOSE_SHANTOU_2216_2005:0.00620784)Node26:0.00253061,PEREGRINEFALCON_HK_D0028_2004:0.0036083)Node25:0.0032889,CK_HK_WF157_2003:0.0066313)Node24:0.0046553)Node2:0.0116809,(((HUMAN_VIETNAM_CL105_2005:0.00652152,DUCK_VIETNAM_376_2005:0.00787762)Node33:0.00196789,HUMAN_VIETNAM_3062_2004:0.0016414)Node32:0.000312551,MALLARD_VIETNAM_16_2003:0.00324422)Node31:0.000412598)Node1:0.000340091,CHICKEN_CK_160_2005:0.00616834,DUCK_VIETNAM_272_2005:0.0094653)"
170 }
171 },
172 "data partitions":{
173 "0":{
174 "name":"meme.filter.default",
175 "coverage":[
176 [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533, 534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559, 560, 561, 562, 563, 564, 565]
177 ]
178 }
179 },
180 "branch attributes":{
181 "0":{
182 "TREESPARROW_HENAN_1_2004":{
183 "original name":"TREESPARROW_HENAN_1_2004",
184 "Nucleotide GTR":0.01066479252384179,
185 "Global MG94xREV":0.01076673590455662,
186 "EBF site 3 (partition 1)":0.9456096051294662,
187 "EBF site 8 (partition 1)":1162.743096991633,
188 "EBF site 9 (partition 1)":1,
189 "EBF site 10 (partition 1)":218.8691185742497,
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192 "EBF site 16 (partition 1)":0.9451095622554209,
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194 "EBF site 20 (partition 1)":3527.455058707973,
195 "EBF site 21 (partition 1)":176.9630563981623,
196 "EBF site 26 (partition 1)":408.9192237736214,
197 "EBF site 27 (partition 1)":6018.398467534517,
198 "EBF site 28 (partition 1)":1,
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200 "EBF site 33 (partition 1)":1,
201 "EBF site 34 (partition 1)":1,
202 "EBF site 37 (partition 1)":0.05724236634162533,
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392 },
393 "HUMAN_VIETNAM_CL105_2005":{
394 "original name":"HUMAN_VIETNAM_CL105_2005",
395 "Nucleotide GTR":0.005986646270743371,
396 "Global MG94xREV":0.006106211622325468,
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603 },
604 "TREESPARROW_HENAN_4_2004":{
605 "original name":"TREESPARROW_HENAN_4_2004",
606 "Nucleotide GTR":0.004617444843308758,
607 "Global MG94xREV":0.004738487843939769,
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814 },
815 "CHICKEN_HEBEI_326_2005":{
816 "original name":"CHICKEN_HEBEI_326_2005",
817 "Nucleotide GTR":0.01918340076972257,
818 "Global MG94xREV":0.01967816199388366,
819 "EBF site 3 (partition 1)":201.3664072283461,
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1026 "CHICKEN_HONGKONG_915_97":{
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1237 "HUMAN_VIETNAM_3062_2004":{
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1659 "DUCK_HONGKONG_Y283_97":{
1660 "original name":"DUCK_HONGKONG_Y283_97",
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1870 "DUCK_VIETNAM_376_2005":{
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2081 "MALLARD_VIETNAM_16_2003":{
2082 "original name":"MALLARD_VIETNAM_16_2003",
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2292 "CHICKEN_CK_160_2005":{
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2503 "DUCK_GUANGZHOU_20_2005":{
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2925 "SWINE_ANHUI_1_2004":{
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3136 "DUCK_VIETNAM_272_2005":{
3137 "original name":"DUCK_VIETNAM_272_2005",
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3347 "HONGKONG_1_97_98":{
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3557 },
3558 "GOOSE_SHANTOU_2216_2005":{
3559 "original name":"GOOSE_SHANTOU_2216_2005",
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3769 "TREESPARROW_HENAN_3_2004":{
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3980 "PEREGRINEFALCON_HK_D0028_2004":{
3981 "original name":"PEREGRINEFALCON_HK_D0028_2004",
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4191 "TREESPARROW_HENAN_2_2004":{
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4402 "HONGKONG_1_538_97":{
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5033 "Node12":{
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5243 "Node15":{
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7763 "Node4":{
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7973 "Node5":{
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8643 "EBF site 142 (partition 1)":{
8644 "attribute type":"branch label",
8645 "display order":144
8646 },
8647 "EBF site 143 (partition 1)":{
8648 "attribute type":"branch label",
8649 "display order":145
8650 },
8651 "EBF site 145 (partition 1)":{
8652 "attribute type":"branch label",
8653 "display order":147
8654 },
8655 "EBF site 146 (partition 1)":{
8656 "attribute type":"branch label",
8657 "display order":148
8658 },
8659 "EBF site 147 (partition 1)":{
8660 "attribute type":"branch label",
8661 "display order":149
8662 },
8663 "EBF site 150 (partition 1)":{
8664 "attribute type":"branch label",
8665 "display order":152
8666 },
8667 "EBF site 152 (partition 1)":{
8668 "attribute type":"branch label",
8669 "display order":154
8670 },
8671 "EBF site 153 (partition 1)":{
8672 "attribute type":"branch label",
8673 "display order":155
8674 },
8675 "EBF site 154 (partition 1)":{
8676 "attribute type":"branch label",
8677 "display order":156
8678 },
8679 "EBF site 155 (partition 1)":{
8680 "attribute type":"branch label",
8681 "display order":157
8682 },
8683 "EBF site 156 (partition 1)":{
8684 "attribute type":"branch label",
8685 "display order":158
8686 },
8687 "EBF site 157 (partition 1)":{
8688 "attribute type":"branch label",
8689 "display order":159
8690 },
8691 "EBF site 167 (partition 1)":{
8692 "attribute type":"branch label",
8693 "display order":169
8694 },
8695 "EBF site 170 (partition 1)":{
8696 "attribute type":"branch label",
8697 "display order":172
8698 },
8699 "EBF site 171 (partition 1)":{
8700 "attribute type":"branch label",
8701 "display order":173
8702 },
8703 "EBF site 172 (partition 1)":{
8704 "attribute type":"branch label",
8705 "display order":174
8706 },
8707 "EBF site 173 (partition 1)":{
8708 "attribute type":"branch label",
8709 "display order":175
8710 },
8711 "EBF site 175 (partition 1)":{
8712 "attribute type":"branch label",
8713 "display order":177
8714 },
8715 "EBF site 178 (partition 1)":{
8716 "attribute type":"branch label",
8717 "display order":180
8718 },
8719 "EBF site 179 (partition 1)":{
8720 "attribute type":"branch label",
8721 "display order":181
8722 },
8723 "EBF site 181 (partition 1)":{
8724 "attribute type":"branch label",
8725 "display order":183
8726 },
8727 "EBF site 185 (partition 1)":{
8728 "attribute type":"branch label",
8729 "display order":187
8730 },
8731 "EBF site 191 (partition 1)":{
8732 "attribute type":"branch label",
8733 "display order":193
8734 },
8735 "EBF site 195 (partition 1)":{
8736 "attribute type":"branch label",
8737 "display order":197
8738 },
8739 "EBF site 196 (partition 1)":{
8740 "attribute type":"branch label",
8741 "display order":198
8742 },
8743 "EBF site 197 (partition 1)":{
8744 "attribute type":"branch label",
8745 "display order":199
8746 },
8747 "EBF site 200 (partition 1)":{
8748 "attribute type":"branch label",
8749 "display order":202
8750 },
8751 "EBF site 201 (partition 1)":{
8752 "attribute type":"branch label",
8753 "display order":203
8754 },
8755 "EBF site 204 (partition 1)":{
8756 "attribute type":"branch label",
8757 "display order":206
8758 },
8759 "EBF site 206 (partition 1)":{
8760 "attribute type":"branch label",
8761 "display order":208
8762 },
8763 "EBF site 209 (partition 1)":{
8764 "attribute type":"branch label",
8765 "display order":211
8766 },
8767 "EBF site 211 (partition 1)":{
8768 "attribute type":"branch label",
8769 "display order":213
8770 },
8771 "EBF site 212 (partition 1)":{
8772 "attribute type":"branch label",
8773 "display order":214
8774 },
8775 "EBF site 213 (partition 1)":{
8776 "attribute type":"branch label",
8777 "display order":215
8778 },
8779 "EBF site 214 (partition 1)":{
8780 "attribute type":"branch label",
8781 "display order":216
8782 },
8783 "EBF site 217 (partition 1)":{
8784 "attribute type":"branch label",
8785 "display order":219
8786 },
8787 "EBF site 221 (partition 1)":{
8788 "attribute type":"branch label",
8789 "display order":223
8790 },
8791 "EBF site 222 (partition 1)":{
8792 "attribute type":"branch label",
8793 "display order":224
8794 },
8795 "EBF site 224 (partition 1)":{
8796 "attribute type":"branch label",
8797 "display order":226
8798 },
8799 "EBF site 226 (partition 1)":{
8800 "attribute type":"branch label",
8801 "display order":228
8802 },
8803 "EBF site 228 (partition 1)":{
8804 "attribute type":"branch label",
8805 "display order":230
8806 },
8807 "EBF site 230 (partition 1)":{
8808 "attribute type":"branch label",
8809 "display order":232
8810 },
8811 "EBF site 231 (partition 1)":{
8812 "attribute type":"branch label",
8813 "display order":233
8814 },
8815 "EBF site 233 (partition 1)":{
8816 "attribute type":"branch label",
8817 "display order":235
8818 },
8819 "EBF site 235 (partition 1)":{
8820 "attribute type":"branch label",
8821 "display order":237
8822 },
8823 "EBF site 236 (partition 1)":{
8824 "attribute type":"branch label",
8825 "display order":238
8826 },
8827 "EBF site 237 (partition 1)":{
8828 "attribute type":"branch label",
8829 "display order":239
8830 },
8831 "EBF site 240 (partition 1)":{
8832 "attribute type":"branch label",
8833 "display order":242
8834 },
8835 "EBF site 241 (partition 1)":{
8836 "attribute type":"branch label",
8837 "display order":243
8838 },
8839 "EBF site 242 (partition 1)":{
8840 "attribute type":"branch label",
8841 "display order":244
8842 },
8843 "EBF site 250 (partition 1)":{
8844 "attribute type":"branch label",
8845 "display order":252
8846 },
8847 "EBF site 253 (partition 1)":{
8848 "attribute type":"branch label",
8849 "display order":255
8850 },
8851 "EBF site 254 (partition 1)":{
8852 "attribute type":"branch label",
8853 "display order":256
8854 },
8855 "EBF site 256 (partition 1)":{
8856 "attribute type":"branch label",
8857 "display order":258
8858 },
8859 "EBF site 258 (partition 1)":{
8860 "attribute type":"branch label",
8861 "display order":260
8862 },
8863 "EBF site 265 (partition 1)":{
8864 "attribute type":"branch label",
8865 "display order":267
8866 },
8867 "EBF site 268 (partition 1)":{
8868 "attribute type":"branch label",
8869 "display order":270
8870 },
8871 "EBF site 271 (partition 1)":{
8872 "attribute type":"branch label",
8873 "display order":273
8874 },
8875 "EBF site 278 (partition 1)":{
8876 "attribute type":"branch label",
8877 "display order":280
8878 },
8879 "EBF site 279 (partition 1)":{
8880 "attribute type":"branch label",
8881 "display order":281
8882 },
8883 "EBF site 282 (partition 1)":{
8884 "attribute type":"branch label",
8885 "display order":284
8886 },
8887 "EBF site 283 (partition 1)":{
8888 "attribute type":"branch label",
8889 "display order":285
8890 },
8891 "EBF site 288 (partition 1)":{
8892 "attribute type":"branch label",
8893 "display order":290
8894 },
8895 "EBF site 291 (partition 1)":{
8896 "attribute type":"branch label",
8897 "display order":293
8898 },
8899 "EBF site 293 (partition 1)":{
8900 "attribute type":"branch label",
8901 "display order":295
8902 },
8903 "EBF site 296 (partition 1)":{
8904 "attribute type":"branch label",
8905 "display order":298
8906 },
8907 "EBF site 298 (partition 1)":{
8908 "attribute type":"branch label",
8909 "display order":300
8910 },
8911 "EBF site 302 (partition 1)":{
8912 "attribute type":"branch label",
8913 "display order":304
8914 },
8915 "EBF site 304 (partition 1)":{
8916 "attribute type":"branch label",
8917 "display order":306
8918 },
8919 "EBF site 306 (partition 1)":{
8920 "attribute type":"branch label",
8921 "display order":308
8922 },
8923 "EBF site 309 (partition 1)":{
8924 "attribute type":"branch label",
8925 "display order":311
8926 },
8927 "EBF site 311 (partition 1)":{
8928 "attribute type":"branch label",
8929 "display order":313
8930 },
8931 "EBF site 312 (partition 1)":{
8932 "attribute type":"branch label",
8933 "display order":314
8934 },
8935 "EBF site 315 (partition 1)":{
8936 "attribute type":"branch label",
8937 "display order":317
8938 },
8939 "EBF site 317 (partition 1)":{
8940 "attribute type":"branch label",
8941 "display order":319
8942 },
8943 "EBF site 327 (partition 1)":{
8944 "attribute type":"branch label",
8945 "display order":329
8946 },
8947 "EBF site 328 (partition 1)":{
8948 "attribute type":"branch label",
8949 "display order":330
8950 },
8951 "EBF site 329 (partition 1)":{
8952 "attribute type":"branch label",
8953 "display order":331
8954 },
8955 "EBF site 331 (partition 1)":{
8956 "attribute type":"branch label",
8957 "display order":333
8958 },
8959 "EBF site 332 (partition 1)":{
8960 "attribute type":"branch label",
8961 "display order":334
8962 },
8963 "EBF site 336 (partition 1)":{
8964 "attribute type":"branch label",
8965 "display order":338
8966 },
8967 "EBF site 338 (partition 1)":{
8968 "attribute type":"branch label",
8969 "display order":340
8970 },
8971 "EBF site 339 (partition 1)":{
8972 "attribute type":"branch label",
8973 "display order":341
8974 },
8975 "EBF site 341 (partition 1)":{
8976 "attribute type":"branch label",
8977 "display order":343
8978 },
8979 "EBF site 342 (partition 1)":{
8980 "attribute type":"branch label",
8981 "display order":344
8982 },
8983 "EBF site 344 (partition 1)":{
8984 "attribute type":"branch label",
8985 "display order":346
8986 },
8987 "EBF site 348 (partition 1)":{
8988 "attribute type":"branch label",
8989 "display order":350
8990 },
8991 "EBF site 351 (partition 1)":{
8992 "attribute type":"branch label",
8993 "display order":353
8994 },
8995 "EBF site 353 (partition 1)":{
8996 "attribute type":"branch label",
8997 "display order":355
8998 },
8999 "EBF site 354 (partition 1)":{
9000 "attribute type":"branch label",
9001 "display order":356
9002 },
9003 "EBF site 357 (partition 1)":{
9004 "attribute type":"branch label",
9005 "display order":359
9006 },
9007 "EBF site 358 (partition 1)":{
9008 "attribute type":"branch label",
9009 "display order":360
9010 },
9011 "EBF site 361 (partition 1)":{
9012 "attribute type":"branch label",
9013 "display order":363
9014 },
9015 "EBF site 362 (partition 1)":{
9016 "attribute type":"branch label",
9017 "display order":364
9018 },
9019 "EBF site 369 (partition 1)":{
9020 "attribute type":"branch label",
9021 "display order":371
9022 },
9023 "EBF site 375 (partition 1)":{
9024 "attribute type":"branch label",
9025 "display order":377
9026 },
9027 "EBF site 377 (partition 1)":{
9028 "attribute type":"branch label",
9029 "display order":379
9030 },
9031 "EBF site 379 (partition 1)":{
9032 "attribute type":"branch label",
9033 "display order":381
9034 },
9035 "EBF site 433 (partition 1)":{
9036 "attribute type":"branch label",
9037 "display order":435
9038 },
9039 "EBF site 384 (partition 1)":{
9040 "attribute type":"branch label",
9041 "display order":386
9042 },
9043 "EBF site 389 (partition 1)":{
9044 "attribute type":"branch label",
9045 "display order":391
9046 },
9047 "EBF site 403 (partition 1)":{
9048 "attribute type":"branch label",
9049 "display order":405
9050 },
9051 "EBF site 408 (partition 1)":{
9052 "attribute type":"branch label",
9053 "display order":410
9054 },
9055 "EBF site 417 (partition 1)":{
9056 "attribute type":"branch label",
9057 "display order":419
9058 },
9059 "EBF site 424 (partition 1)":{
9060 "attribute type":"branch label",
9061 "display order":426
9062 },
9063 "EBF site 429 (partition 1)":{
9064 "attribute type":"branch label",
9065 "display order":431
9066 },
9067 "EBF site 431 (partition 1)":{
9068 "attribute type":"branch label",
9069 "display order":433
9070 },
9071 "EBF site 440 (partition 1)":{
9072 "attribute type":"branch label",
9073 "display order":442
9074 },
9075 "EBF site 441 (partition 1)":{
9076 "attribute type":"branch label",
9077 "display order":443
9078 },
9079 "EBF site 445 (partition 1)":{
9080 "attribute type":"branch label",
9081 "display order":447
9082 },
9083 "EBF site 454 (partition 1)":{
9084 "attribute type":"branch label",
9085 "display order":456
9086 },
9087 "EBF site 462 (partition 1)":{
9088 "attribute type":"branch label",
9089 "display order":464
9090 },
9091 "EBF site 466 (partition 1)":{
9092 "attribute type":"branch label",
9093 "display order":468
9094 },
9095 "EBF site 471 (partition 1)":{
9096 "attribute type":"branch label",
9097 "display order":473
9098 },
9099 "EBF site 473 (partition 1)":{
9100 "attribute type":"branch label",
9101 "display order":475
9102 },
9103 "EBF site 477 (partition 1)":{
9104 "attribute type":"branch label",
9105 "display order":479
9106 },
9107 "EBF site 478 (partition 1)":{
9108 "attribute type":"branch label",
9109 "display order":480
9110 },
9111 "EBF site 485 (partition 1)":{
9112 "attribute type":"branch label",
9113 "display order":487
9114 },
9115 "EBF site 479 (partition 1)":{
9116 "attribute type":"branch label",
9117 "display order":481
9118 },
9119 "EBF site 481 (partition 1)":{
9120 "attribute type":"branch label",
9121 "display order":483
9122 },
9123 "EBF site 488 (partition 1)":{
9124 "attribute type":"branch label",
9125 "display order":490
9126 },
9127 "EBF site 489 (partition 1)":{
9128 "attribute type":"branch label",
9129 "display order":491
9130 },
9131 "EBF site 492 (partition 1)":{
9132 "attribute type":"branch label",
9133 "display order":494
9134 },
9135 "EBF site 494 (partition 1)":{
9136 "attribute type":"branch label",
9137 "display order":496
9138 },
9139 "EBF site 499 (partition 1)":{
9140 "attribute type":"branch label",
9141 "display order":501
9142 },
9143 "EBF site 500 (partition 1)":{
9144 "attribute type":"branch label",
9145 "display order":502
9146 },
9147 "EBF site 506 (partition 1)":{
9148 "attribute type":"branch label",
9149 "display order":508
9150 },
9151 "EBF site 507 (partition 1)":{
9152 "attribute type":"branch label",
9153 "display order":509
9154 },
9155 "EBF site 508 (partition 1)":{
9156 "attribute type":"branch label",
9157 "display order":510
9158 },
9159 "EBF site 509 (partition 1)":{
9160 "attribute type":"branch label",
9161 "display order":511
9162 },
9163 "EBF site 513 (partition 1)":{
9164 "attribute type":"branch label",
9165 "display order":515
9166 },
9167 "EBF site 514 (partition 1)":{
9168 "attribute type":"branch label",
9169 "display order":516
9170 },
9171 "EBF site 515 (partition 1)":{
9172 "attribute type":"branch label",
9173 "display order":517
9174 },
9175 "EBF site 519 (partition 1)":{
9176 "attribute type":"branch label",
9177 "display order":521
9178 },
9179 "EBF site 527 (partition 1)":{
9180 "attribute type":"branch label",
9181 "display order":529
9182 },
9183 "EBF site 529 (partition 1)":{
9184 "attribute type":"branch label",
9185 "display order":531
9186 },
9187 "EBF site 537 (partition 1)":{
9188 "attribute type":"branch label",
9189 "display order":539
9190 },
9191 "EBF site 538 (partition 1)":{
9192 "attribute type":"branch label",
9193 "display order":540
9194 },
9195 "EBF site 539 (partition 1)":{
9196 "attribute type":"branch label",
9197 "display order":541
9198 },
9199 "EBF site 540 (partition 1)":{
9200 "attribute type":"branch label",
9201 "display order":542
9202 },
9203 "EBF site 544 (partition 1)":{
9204 "attribute type":"branch label",
9205 "display order":546
9206 },
9207 "EBF site 545 (partition 1)":{
9208 "attribute type":"branch label",
9209 "display order":547
9210 },
9211 "EBF site 549 (partition 1)":{
9212 "attribute type":"branch label",
9213 "display order":551
9214 },
9215 "EBF site 553 (partition 1)":{
9216 "attribute type":"branch label",
9217 "display order":555
9218 },
9219 "EBF site 558 (partition 1)":{
9220 "attribute type":"branch label",
9221 "display order":560
9222 },
9223 "EBF site 560 (partition 1)":{
9224 "attribute type":"branch label",
9225 "display order":562
9226 },
9227 "EBF site 564 (partition 1)":{
9228 "attribute type":"branch label",
9229 "display order":566
9230 }
9231 }
9232 },
9233 "MLE":{
9234 "headers":[
9235 ["alpha;", "Synonymous substitution rate at a site"],
9236 ["&beta;<sup>-</sup>", "Non-synonymous substitution rate at a site for the negative/neutral evolution component"],
9237 ["p<sup>-</sup>", "Mixture distribution weight allocated to &beta;<sup>-</sup>; loosely -- the proportion of the tree evolving neutrally or under negative selection"],
9238 ["&beta;<sup>+</sup>", "Non-synonymous substitution rate at a site for the positive/neutral evolution component"],
9239 ["p<sup>+</sup>", "Mixture distribution weight allocated to &beta;<sup>+</sup>; loosely -- the proportion of the tree evolving neutrally or under positive selection"],
9240 ["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p<sup>+</sup> &gt; 0 <emph>and<emph> &beta;<sup>+</sup> &gt; &alpha;"],
9241 ["p-value", "Asymptotic p-value for episodic diversification, i.e., p<sup>+</sup> &gt; 0 <emph>and<emph> &beta;<sup>+</sup> &gt; &alpha;"],
9242 ["# 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"],
9243 ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
9244 ],
9245 "content":{
9246 "0":[
9247 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9248 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9249 [3.518153136581004e-17, 3.243045519502881e-17, 1.022166200682819e-08, 1.291751771813077, 0.999999989778338, 0.5894186108086057, 0.4058674930166563, 1, 0.3590955405423049],
9250 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9251 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9252 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9253 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9254 [0, 0, 1.015244473805534e-08, 2.805293595854978, 0.9999999898475552, 1.564165559839974, 0.2310493931422519, 2, 0.7798467493791119],
9255 [3.097517451103013, 3.633546560692318e-13, 0.006739028294327419, 0, 0.9932609717056726, 0, 0.6666666666666666, 0, 0.3592491319023247],
9256 [0, 0, 1.066894692458495e-08, 2.051552228725943, 0.9999999893310531, 0.4229558324457479, 0.4514150344986089, 1, 0.5703133313001572],
9257 [0, 0, 1.001269178443788e-08, 3.944223233914665, 0.9999999899873082, 2.43042776936683, 0.144470531376273, 1, 1.096459091757323],
9258 [4.145693582901539, 1.893694670765467, 1, 1.728430979317008, 0, 0, 0.6666666666666666, 0, 1.007246616185795],
9259 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9260 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9261 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9262 [6.93484933547672e-17, 6.392567688995331e-17, 1.030030625693157e-08, 0.9290606906239126, 0.9999999896996937, 0.429003806262461, 0.4496226523843093, 1, 0.2582706353881744],
9263 [4.073331916826687, 1.964429091966281e-13, 0.006739408681290566, 0, 0.9932605913187095, 0, 0.6666666666666666, 0, 0.4724237968534862],
9264 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9265 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9266 [3.184654870622172e-17, 2.935625684381423e-17, 0.09528354227571036, 1.23415455927649, 0.9047164577242897, 0.5820726852114504, 0.4077294328402945, 1, 0.310393767954204],
9267 [0, 0, 1.014329318303121e-08, 2.542043848640683, 0.9999999898567068, 1.389862633564338, 0.2545350229851194, 1, 0.7066656534948396],
9268 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9269 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9270 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9271 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9272 [0, 0, 1.128981602688825e-08, 1.197915132727622, 0.9999999887101839, 0.6174695851256686, 0.3988677672174981, 1, 0.3330097864293045],
9273 [7.859751593667559e-17, 7.245145734338422e-17, 0.6054123585982152, 3.355057384083219, 0.3945876414017848, 0.6574696688520838, 0.3891754851636057, 1, 0.3680225090745513],
9274 [4.281650170441328, 1.700811001215517e-13, 0.01799487943873323, 0, 0.9820051205612668, 0, 0.6666666666666666, 0, 0.4965844845499574],
9275 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9276 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9277 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9278 [0, 0, 0.2039072184606198, 1.54490396548033, 0.7960927815393802, 0.7575357890719587, 0.3662885611320149, 1, 0.3418976567710703],
9279 [3.450387565388855, 2.778481054513338e-13, 0.006740436271927257, 0, 0.9932595637280728, 0, 0.6666666666666666, 0, 0.4001749004355483],
9280 [2.951752532329065, 5.891628767012343e-15, 0.01796479182207459, 0, 0.9820352081779254, 0, 0.6666666666666666, 0, 0.3423433609557532],
9281 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9282 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9283 [7.356813916278453e-16, 7.070430622089884e-16, 0.9652398501401529, 347.6427247535747, 0.0347601498598471, 2.744506410024989, 0.1222396136895078, 1, 3.359276375078736],
9284 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9285 [7.452741291360716, 7.639496412166912e-16, 0.2818805293849745, 0, 0.7181194706150256, 0, 0.6666666666666666, 0, 0.8643666683009437],
9286 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9287 [0, 0, 1, 0, 0, 0, 1, 0, 0],
9288 [0, 0, 1, 0, 0, 0, 1, 0, 0],
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9813 ]
9814 }
9815 }
9816 }