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view test-data/meme-out1.json @ 0:fe399429a5d2 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 04:22:54 -0500
parents
children 0f108ee932ea
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{
 "analysis":{
   "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    ",
   "version":"2.0.1",
   "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.",
   "authors":"Sergei L. Kosakovsky Pond, Steven Weaver",
   "contact":"spond@temple.edu",
   "requirements":"in-frame codon alignment and a phylogenetic tree"
  },
 "fits":{
   "Nucleotide GTR":{
     "Log Likelihood":-4394.17778442101,
     "estimated parameters":47,
     "AIC-c":8882.482274823486,
     "Equilibrium frequencies":[
      [0.3460163217230355],
      [0.1876507375623983],
      [0.2296889898480005],
      [0.2366439508665657]
      ],
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0.1602243049428088,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0.1350661843114337,
       "Substitution rate from nucleotide C to nucleotide G":0.04669906431175039,
       "Substitution rate from nucleotide C to nucleotide T":1.290725939052547,
       "Substitution rate from nucleotide G to nucleotide T":0.1442807316736102
      },
     "display order":0
    },
   "Global MG94xREV":{
     "Log Likelihood":-4272.739394378317,
     "estimated parameters":54,
     "AIC-c":8653.980859587502,
     "Equilibrium frequencies":[
      [0.04794212053691846],
      [0.02918423386756777],
      [0.03061835466109362],
      [0.03395226455636327],
      [0.02063374857573568],
      [0.01256056547467788],
      [0.01317779490778274],
      [0.01461267216775245],
      [0.02309512129134449],
      [0.01405889880167917],
      [0.01474975672164567],
      [0.01635579860179934],
      [0.03032452824999034],
      [0.01845972006369387],
      [0.01936683547765817],
      [0.02147561255447049],
      [0.02137643485619778],
      [0.01301266750638816],
      [0.01365211335015547],
      [0.01513863724385318],
      [0.009200176740799796],
      [0.005600505497450756],
      [0.005875715784779066],
      [0.006515498921838312],
      [0.01029765371767897],
      [0.006268582428525358],
      [0.0065766221888793],
      [0.007292724214466442],
      [0.01352110201678854],
      [0.00823082081030041],
      [0.008635285471781717],
      [0.009575547089413102],
      [0.03891475766269277],
      [0.02368892689369449],
      [0.02485300688252417],
      [0.02755915117048418],
      [0.01674847329457107],
      [0.01019544726180969],
      [0.01069645417478218],
      [0.01186114818960848],
      [0.0187463766345312],
      [0.01141164874946168],
      [0.01197242011780667],
      [0.01327604894903844],
      [0.02461450713626915],
      [0.01498380807429274],
      [0.01572011627491417],
      [0.01743181671681681],
      [0.02096427272215724],
      [0.0243893513506083],
      [0.01482209656025475],
      [0.009022786801619234],
      [0.009466168876559794],
      [0.0104969020572672],
      [0.01009910316608133],
      [0.0105953757052942],
      [0.01174906369078435],
      [0.02178339453036125],
      [0.01326039969204127],
      [0.01391201915942615],
      [0.01542684315477715]
      ],
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *test*":[
        [0.2936035676191999, 1]
        ]
      },
     "display order":1
    }
  },
 "timers":{
   "Total time":{
     "timer":816,
     "order":0
    },
   "Model fitting":{
     "timer":12,
     "order":1
    },
   "MEME analysis":{
     "timer":803,
     "order":2
    }
  },
 "tested":{
   "0":{
     "TREESPARROW_HENAN_1_2004":"test",
     "TREESPARROW_HENAN_3_2004":"test",
     "Node6":"test",
     "TREESPARROW_HENAN_4_2004":"test",
     "Node5":"test",
     "CHICKEN_HEBEI_326_2005":"test",
     "SWINE_ANHUI_1_2004":"test",
     "TREESPARROW_HENAN_2_2004":"test",
     "Node12":"test",
     "Node10":"test",
     "Node4":"test",
     "CHICKEN_HONGKONG_915_97":"test",
     "GOOSE_HONGKONG_W355_97":"test",
     "DUCK_HONGKONG_Y283_97":"test",
     "Node19":"test",
     "Node17":"test",
     "HONGKONG_1_97_98":"test",
     "Node16":"test",
     "HONGKONG_1_538_97":"test",
     "Node15":"test",
     "Node3":"test",
     "DUCK_GUANGZHOU_20_2005":"test",
     "GOOSE_SHANTOU_2216_2005":"test",
     "Node26":"test",
     "PEREGRINEFALCON_HK_D0028_2004":"test",
     "Node25":"test",
     "CK_HK_WF157_2003":"test",
     "Node24":"test",
     "Node2":"test",
     "HUMAN_VIETNAM_CL105_2005":"test",
     "DUCK_VIETNAM_376_2005":"test",
     "Node33":"test",
     "HUMAN_VIETNAM_3062_2004":"test",
     "Node32":"test",
     "MALLARD_VIETNAM_16_2003":"test",
     "Node31":"test",
     "Node1":"test",
     "CHICKEN_CK_160_2005":"test",
     "DUCK_VIETNAM_272_2005":"test"
    }
  },
 "input":{
   "file name":"/tmp/tmpv_gXOY/job_working_directory/002/2719/working/meme_input.fa",
   "number of sequences":21,
   "number of sites":566,
   "partition count":1,
   "trees":{
     "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)"
    }
  },
 "data partitions":{
   "0":{
     "name":"meme.filter.default",
     "coverage":[
      [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 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]
      ]
    }
  },
 "branch attributes":{
   "0":{
     "TREESPARROW_HENAN_1_2004":{
       "original name":"TREESPARROW_HENAN_1_2004",
       "Nucleotide GTR":0.01066479252384179,
       "Global MG94xREV":0.01076673590455662,
       "EBF site 3 (partition 1)":0.9456096051294662,
       "EBF site 8 (partition 1)":1162.743096991633,
       "EBF site 9 (partition 1)":1,
       "EBF site 10 (partition 1)":218.8691185742497,
       "EBF site 11 (partition 1)":127.9229379574454,
       "EBF site 12 (partition 1)":1,
       "EBF site 16 (partition 1)":0.9451095622554209,
       "EBF site 17 (partition 1)":1,
       "EBF site 20 (partition 1)":3527.455058707973,
       "EBF site 21 (partition 1)":176.9630563981623,
       "EBF site 26 (partition 1)":408.9192237736214,
       "EBF site 27 (partition 1)":6018.398467534517,
       "EBF site 28 (partition 1)":1,
       "EBF site 32 (partition 1)":3526.472765483446,
       "EBF site 33 (partition 1)":1,
       "EBF site 34 (partition 1)":1,
       "EBF site 37 (partition 1)":0.05724236634162533,
       "EBF site 39 (partition 1)":1,
       "EBF site 45 (partition 1)":1,
       "EBF site 49 (partition 1)":1,
       "EBF site 50 (partition 1)":1,
       "EBF site 51 (partition 1)":0.9481415983525313,
       "EBF site 52 (partition 1)":1,
       "EBF site 54 (partition 1)":1,
       "EBF site 58 (partition 1)":1,
       "EBF site 59 (partition 1)":1,
       "EBF site 60 (partition 1)":0.9841498071715201,
       "EBF site 61 (partition 1)":0.9461884386551284,
       "EBF site 62 (partition 1)":1,
       "EBF site 64 (partition 1)":1,
       "EBF site 66 (partition 1)":1,
       "EBF site 68 (partition 1)":1,
       "EBF site 69 (partition 1)":1,
       "EBF site 70 (partition 1)":1,
       "EBF site 73 (partition 1)":1,
       "EBF site 77 (partition 1)":1,
       "EBF site 78 (partition 1)":1,
       "EBF site 79 (partition 1)":1,
       "EBF site 80 (partition 1)":1,
       "EBF site 81 (partition 1)":1,
       "EBF site 84 (partition 1)":1,
       "EBF site 86 (partition 1)":1,
       "EBF site 89 (partition 1)":1,
       "EBF site 91 (partition 1)":1,
       "EBF site 99 (partition 1)":0.8934318436198261,
       "EBF site 100 (partition 1)":0.8359286168349669,
       "EBF site 102 (partition 1)":0.840682336279177,
       "EBF site 104 (partition 1)":0.9467648993042056,
       "EBF site 107 (partition 1)":1,
       "EBF site 109 (partition 1)":1,
       "EBF site 110 (partition 1)":0.8930664337623379,
       "EBF site 112 (partition 1)":1,
       "EBF site 113 (partition 1)":0.5077191311825521,
       "EBF site 117 (partition 1)":1,
       "EBF site 128 (partition 1)":1,
       "EBF site 131 (partition 1)":0.9328416754118536,
       "EBF site 136 (partition 1)":1,
       "EBF site 139 (partition 1)":0.9441408488814703,
       "EBF site 140 (partition 1)":1,
       "EBF site 142 (partition 1)":0.8500709198156691,
       "EBF site 143 (partition 1)":0.4787687912682837,
       "EBF site 145 (partition 1)":0.9422395930999242,
       "EBF site 146 (partition 1)":1,
       "EBF site 147 (partition 1)":1,
       "EBF site 150 (partition 1)":0.8931764248571649,
       "EBF site 152 (partition 1)":1,
       "EBF site 153 (partition 1)":1,
       "EBF site 154 (partition 1)":2.032970366525119,
       "EBF site 155 (partition 1)":1,
       "EBF site 156 (partition 1)":0.7605408968194968,
       "EBF site 157 (partition 1)":0.7923889003403327,
       "EBF site 167 (partition 1)":0.3224823721470498,
       "EBF site 170 (partition 1)":1,
       "EBF site 171 (partition 1)":0.8937282882888197,
       "EBF site 172 (partition 1)":0.8334353179208003,
       "EBF site 173 (partition 1)":1,
       "EBF site 175 (partition 1)":1,
       "EBF site 178 (partition 1)":0.3319155013530999,
       "EBF site 179 (partition 1)":140.8487463162621,
       "EBF site 181 (partition 1)":1,
       "EBF site 185 (partition 1)":0.0250008957377292,
       "EBF site 191 (partition 1)":0.8868823751410472,
       "EBF site 195 (partition 1)":1,
       "EBF site 196 (partition 1)":1,
       "EBF site 197 (partition 1)":1,
       "EBF site 200 (partition 1)":0.9453963832021259,
       "EBF site 201 (partition 1)":0.8954929105407161,
       "EBF site 204 (partition 1)":0.7888293115681604,
       "EBF site 206 (partition 1)":1,
       "EBF site 209 (partition 1)":1,
       "EBF site 211 (partition 1)":0.8928661765804535,
       "EBF site 212 (partition 1)":1,
       "EBF site 213 (partition 1)":1,
       "EBF site 214 (partition 1)":0.3116750951954585,
       "EBF site 217 (partition 1)":1,
       "EBF site 221 (partition 1)":1,
       "EBF site 222 (partition 1)":1,
       "EBF site 224 (partition 1)":1,
       "EBF site 226 (partition 1)":1,
       "EBF site 228 (partition 1)":0.9012061988166143,
       "EBF site 230 (partition 1)":1,
       "EBF site 231 (partition 1)":1,
       "EBF site 233 (partition 1)":0.9471342563727014,
       "EBF site 235 (partition 1)":0.9355047056039391,
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       "EBF site 240 (partition 1)":1,
       "EBF site 241 (partition 1)":1,
       "EBF site 242 (partition 1)":0.9364515816021974,
       "EBF site 250 (partition 1)":1,
       "EBF site 253 (partition 1)":1,
       "EBF site 254 (partition 1)":1,
       "EBF site 256 (partition 1)":1,
       "EBF site 258 (partition 1)":0.9467463555281146,
       "EBF site 265 (partition 1)":1,
       "EBF site 268 (partition 1)":1,
       "EBF site 271 (partition 1)":1,
       "EBF site 278 (partition 1)":1,
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       "EBF site 282 (partition 1)":1,
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       "EBF site 288 (partition 1)":1,
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       "EBF site 293 (partition 1)":1,
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       "EBF site 309 (partition 1)":1,
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       "EBF site 315 (partition 1)":0.9464963596829592,
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       "EBF site 327 (partition 1)":1,
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       "EBF site 336 (partition 1)":0.06308355401293796,
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       "EBF site 433 (partition 1)":1,
       "EBF site 384 (partition 1)":0.8907110686456686,
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       "EBF site 403 (partition 1)":0.9461751178690665,
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       "EBF site 440 (partition 1)":1,
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       "EBF site 462 (partition 1)":0.9010976189752229,
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       "EBF site 489 (partition 1)":0.9464165621810909,
       "EBF site 492 (partition 1)":0.870750294987559,
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       "EBF site 499 (partition 1)":0.3780885375135474,
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       "EBF site 514 (partition 1)":1,
       "EBF site 515 (partition 1)":0.1497914471070693,
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       "EBF site 527 (partition 1)":0.8986165376570547,
       "EBF site 529 (partition 1)":0.9459902784942635,
       "EBF site 537 (partition 1)":1,
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       "EBF site 560 (partition 1)":1,
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      },
     "HUMAN_VIETNAM_CL105_2005":{
       "original name":"HUMAN_VIETNAM_CL105_2005",
       "Nucleotide GTR":0.005986646270743371,
       "Global MG94xREV":0.006106211622325468,
       "EBF site 3 (partition 1)":0.968616063973319,
       "EBF site 8 (partition 1)":0.9345724676222895,
       "EBF site 9 (partition 1)":1,
       "EBF site 10 (partition 1)":0.9367014431890973,
       "EBF site 11 (partition 1)":0.9045043782491251,
       "EBF site 12 (partition 1)":1,
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     "TREESPARROW_HENAN_4_2004":{
       "original name":"TREESPARROW_HENAN_4_2004",
       "Nucleotide GTR":0.004617444843308758,
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     "CHICKEN_HEBEI_326_2005":{
       "original name":"CHICKEN_HEBEI_326_2005",
       "Nucleotide GTR":0.01918340076972257,
       "Global MG94xREV":0.01967816199388366,
       "EBF site 3 (partition 1)":201.3664072283461,
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     "CHICKEN_HONGKONG_915_97":{
       "original name":"CHICKEN_HONGKONG_915_97",
       "Nucleotide GTR":0.0005887016536874224,
       "Global MG94xREV":0.0005957378711334177,
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     "HUMAN_VIETNAM_3062_2004":{
       "original name":"HUMAN_VIETNAM_3062_2004",
       "Nucleotide GTR":0.001781425550267506,
       "Global MG94xREV":0.001793576016824539,
       "EBF site 3 (partition 1)":0.9906300263401322,
       "EBF site 8 (partition 1)":0.9802039169342038,
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     "DUCK_VIETNAM_376_2005":{
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       "Nucleotide GTR":0.008353464800246744,
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     "MALLARD_VIETNAM_16_2003":{
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       "Nucleotide GTR":0.00355551262918992,
       "Global MG94xREV":0.003602318751584569,
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     "CHICKEN_CK_160_2005":{
       "original name":"CHICKEN_CK_160_2005",
       "Nucleotide GTR":0.006564644089644057,
       "Global MG94xREV":0.006696317239039201,
       "EBF site 3 (partition 1)":0.9656566441068151,
       "EBF site 8 (partition 1)":0.9285284291514248,
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       "EBF site 11 (partition 1)":0.8958984487588691,
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       "EBF site 37 (partition 1)":0.08000394285014073,
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     "DUCK_GUANGZHOU_20_2005":{
       "original name":"DUCK_GUANGZHOU_20_2005",
       "Nucleotide GTR":0.006543973858645086,
       "Global MG94xREV":0.006650482064933933,
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     "CK_HK_WF157_2003":{
       "original name":"CK_HK_WF157_2003",
       "Nucleotide GTR":0.006579217513757813,
       "Global MG94xREV":0.006689704249997951,
       "EBF site 3 (partition 1)":0.9656909091743442,
       "EBF site 8 (partition 1)":0.9321266099815247,
       "EBF site 9 (partition 1)":1,
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       "EBF site 11 (partition 1)":0.8960515948322754,
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     "SWINE_ANHUI_1_2004":{
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     "DUCK_VIETNAM_272_2005":{
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     "HONGKONG_1_97_98":{
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     "GOOSE_SHANTOU_2216_2005":{
       "original name":"GOOSE_SHANTOU_2216_2005",
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     "TREESPARROW_HENAN_3_2004":{
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     "PEREGRINEFALCON_HK_D0028_2004":{
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     "TREESPARROW_HENAN_2_2004":{
       "original name":"TREESPARROW_HENAN_2_2004",
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       "EBF site 560 (partition 1)":1,
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     "HONGKONG_1_538_97":{
       "original name":"HONGKONG_1_538_97",
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       "Global MG94xREV":0,
       "EBF site 3 (partition 1)":1.000000004454476,
       "EBF site 8 (partition 1)":0.9999999964832573,
       "EBF site 9 (partition 1)":1,
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       "EBF site 60 (partition 1)":1.000000001960442,
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     "Node1":{
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       "EBF site 3 (partition 1)":0.994240864755329,
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     "Node12":{
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     "Node2":{
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     "Node25":{
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     "Node4":{
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     "Node5":{
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     "EBF site 104 (partition 1)":{
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     "EBF site 156 (partition 1)":{
       "attribute type":"branch label",
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     "EBF site 157 (partition 1)":{
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     "EBF site 167 (partition 1)":{
       "attribute type":"branch label",
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     "EBF site 170 (partition 1)":{
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     "EBF site 171 (partition 1)":{
       "attribute type":"branch label",
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     "EBF site 172 (partition 1)":{
       "attribute type":"branch label",
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     "EBF site 173 (partition 1)":{
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     "EBF site 175 (partition 1)":{
       "attribute type":"branch label",
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     "EBF site 178 (partition 1)":{
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     "EBF site 179 (partition 1)":{
       "attribute type":"branch label",
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     "EBF site 181 (partition 1)":{
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       "attribute type":"branch label",
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     "EBF site 195 (partition 1)":{
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     "EBF site 196 (partition 1)":{
       "attribute type":"branch label",
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     "EBF site 197 (partition 1)":{
       "attribute type":"branch label",
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     "EBF site 200 (partition 1)":{
       "attribute type":"branch label",
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       "attribute type":"branch label",
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     "EBF site 204 (partition 1)":{
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     "EBF site 206 (partition 1)":{
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     "EBF site 209 (partition 1)":{
       "attribute type":"branch label",
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     "EBF site 213 (partition 1)":{
       "attribute type":"branch label",
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     "EBF site 214 (partition 1)":{
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     "EBF site 217 (partition 1)":{
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     "EBF site 224 (partition 1)":{
       "attribute type":"branch label",
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     "EBF site 228 (partition 1)":{
       "attribute type":"branch label",
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     "EBF site 241 (partition 1)":{
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     "EBF site 242 (partition 1)":{
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     "EBF site 250 (partition 1)":{
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     "EBF site 253 (partition 1)":{
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     "EBF site 254 (partition 1)":{
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     "EBF site 256 (partition 1)":{
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     "EBF site 258 (partition 1)":{
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     "EBF site 265 (partition 1)":{
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     "EBF site 268 (partition 1)":{
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     "EBF site 271 (partition 1)":{
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     "EBF site 278 (partition 1)":{
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     "EBF site 288 (partition 1)":{
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     "EBF site 311 (partition 1)":{
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     "EBF site 312 (partition 1)":{
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     "EBF site 317 (partition 1)":{
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     "EBF site 328 (partition 1)":{
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     "EBF site 329 (partition 1)":{
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     "EBF site 375 (partition 1)":{
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     "EBF site 377 (partition 1)":{
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     "EBF site 379 (partition 1)":{
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     "EBF site 384 (partition 1)":{
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     "EBF site 389 (partition 1)":{
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     "EBF site 403 (partition 1)":{
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     "EBF site 408 (partition 1)":{
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     "EBF site 417 (partition 1)":{
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     "EBF site 424 (partition 1)":{
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     "EBF site 429 (partition 1)":{
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     "EBF site 431 (partition 1)":{
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     "EBF site 440 (partition 1)":{
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     "EBF site 441 (partition 1)":{
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     "EBF site 445 (partition 1)":{
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     "EBF site 454 (partition 1)":{
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     "EBF site 462 (partition 1)":{
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     "EBF site 466 (partition 1)":{
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     "EBF site 471 (partition 1)":{
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     "EBF site 473 (partition 1)":{
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     "EBF site 477 (partition 1)":{
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     "EBF site 478 (partition 1)":{
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     "EBF site 485 (partition 1)":{
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     "EBF site 479 (partition 1)":{
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     "EBF site 481 (partition 1)":{
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     "EBF site 488 (partition 1)":{
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     "EBF site 489 (partition 1)":{
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     "EBF site 492 (partition 1)":{
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     "EBF site 494 (partition 1)":{
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     "EBF site 499 (partition 1)":{
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     "EBF site 500 (partition 1)":{
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     "EBF site 506 (partition 1)":{
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     "EBF site 507 (partition 1)":{
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     "EBF site 508 (partition 1)":{
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     "EBF site 509 (partition 1)":{
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     "EBF site 513 (partition 1)":{
       "attribute type":"branch label",
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     "EBF site 514 (partition 1)":{
       "attribute type":"branch label",
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     "EBF site 515 (partition 1)":{
       "attribute type":"branch label",
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      },
     "EBF site 519 (partition 1)":{
       "attribute type":"branch label",
       "display order":521
      },
     "EBF site 527 (partition 1)":{
       "attribute type":"branch label",
       "display order":529
      },
     "EBF site 529 (partition 1)":{
       "attribute type":"branch label",
       "display order":531
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     "EBF site 537 (partition 1)":{
       "attribute type":"branch label",
       "display order":539
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     "EBF site 538 (partition 1)":{
       "attribute type":"branch label",
       "display order":540
      },
     "EBF site 539 (partition 1)":{
       "attribute type":"branch label",
       "display order":541
      },
     "EBF site 540 (partition 1)":{
       "attribute type":"branch label",
       "display order":542
      },
     "EBF site 544 (partition 1)":{
       "attribute type":"branch label",
       "display order":546
      },
     "EBF site 545 (partition 1)":{
       "attribute type":"branch label",
       "display order":547
      },
     "EBF site 549 (partition 1)":{
       "attribute type":"branch label",
       "display order":551
      },
     "EBF site 553 (partition 1)":{
       "attribute type":"branch label",
       "display order":555
      },
     "EBF site 558 (partition 1)":{
       "attribute type":"branch label",
       "display order":560
      },
     "EBF site 560 (partition 1)":{
       "attribute type":"branch label",
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     "EBF site 564 (partition 1)":{
       "attribute type":"branch label",
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    }
  },
 "MLE":{
   "headers":[
    ["alpha;", "Synonymous substitution rate at a site"],
    ["&beta;<sup>-</sup>", "Non-synonymous substitution rate at a site for the negative/neutral evolution component"],
    ["p<sup>-</sup>", "Mixture distribution weight allocated to &beta;<sup>-</sup>; loosely -- the proportion of the tree evolving neutrally or under negative selection"],
    ["&beta;<sup>+</sup>", "Non-synonymous substitution rate at a site for the positive/neutral evolution component"],
    ["p<sup>+</sup>", "Mixture distribution weight allocated to &beta;<sup>+</sup>; loosely -- the proportion of the tree evolving neutrally or under positive selection"],
    ["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p<sup>+</sup> &gt; 0 <emph>and<emph> &beta;<sup>+</sup> &gt; &alpha;"],
    ["p-value", "Asymptotic p-value for episodic diversification, i.e., p<sup>+</sup> &gt; 0 <emph>and<emph> &beta;<sup>+</sup> &gt; &alpha;"],
    ["# 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"],
    ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
    ],
   "content":{
     "0":[
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      [0, 0, 1.001269178443788e-08, 3.944223233914665, 0.9999999899873082, 2.43042776936683, 0.144470531376273, 1, 1.096459091757323],
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      [6.93484933547672e-17, 6.392567688995331e-17, 1.030030625693157e-08, 0.9290606906239126, 0.9999999896996937, 0.429003806262461, 0.4496226523843093, 1, 0.2582706353881744],
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      [0, 0, 1.014329318303121e-08, 2.542043848640683, 0.9999999898567068, 1.389862633564338, 0.2545350229851194, 1, 0.7066656534948396],
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      [7.859751593667559e-17, 7.245145734338422e-17, 0.6054123585982152, 3.355057384083219, 0.3945876414017848, 0.6574696688520838, 0.3891754851636057, 1, 0.3680225090745513],
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      [7.356813916278453e-16, 7.070430622089884e-16, 0.9652398501401529, 347.6427247535747, 0.0347601498598471, 2.744506410024989, 0.1222396136895078, 1, 3.359276375078736],
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