view test-data/meme-out1.json @ 3:fb40b0928cad draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
author iuc
date Fri, 14 Feb 2020 16:44:41 -0500
parents 5c87e4907e08
children f73435dc282b
line wrap: on
line source

{
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      [0, 0, 1, 0, 0, 0, 1, 0, 0],
      [0, 0, 1, 0, 0, 0, 1, 0, 0] 
      ]
    },
   "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"] 
    ]
  },
 "analysis":{
   "authors":"Sergei L. Kosakovsky Pond, Steven Weaver",
   "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.",
   "contact":"spond@temple.edu",
   "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    ",
   "requirements":"in-frame codon alignment and a phylogenetic tree",
   "version":"2.1.1"
  },
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       "original name":"CHICKEN_CK_160_2005"
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       "original name":"CHICKEN_HEBEI_326_2005"
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       "EBF site 86 (partition 1)":1,
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       "EBF site 99 (partition 1)":0.9260580476744792,
       "Global MG94xREV":0.004315099710833928,
       "Nucleotide GTR":0.004255811615041097,
       "original name":"HONGKONG_1_97_98"
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     "HUMAN_VIETNAM_3062_2004":{
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     "HUMAN_VIETNAM_CL105_2005":{
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       "Global MG94xREV":0.003602587208878145,
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       "original name":"MALLARD_VIETNAM_16_2003"
      },
     "Node10":{
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     "PEREGRINEFALCON_HK_D0028_2004":{
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       "attribute type":"branch label",
       "display order":52
      },
     "EBF site 506 (partition 1)":{
       "attribute type":"branch label",
       "display order":508
      },
     "EBF site 507 (partition 1)":{
       "attribute type":"branch label",
       "display order":509
      },
     "EBF site 509 (partition 1)":{
       "attribute type":"branch label",
       "display order":511
      },
     "EBF site 51 (partition 1)":{
       "attribute type":"branch label",
       "display order":53
      },
     "EBF site 513 (partition 1)":{
       "attribute type":"branch label",
       "display order":515
      },
     "EBF site 514 (partition 1)":{
       "attribute type":"branch label",
       "display order":516
      },
     "EBF site 515 (partition 1)":{
       "attribute type":"branch label",
       "display order":517
      },
     "EBF site 519 (partition 1)":{
       "attribute type":"branch label",
       "display order":521
      },
     "EBF site 52 (partition 1)":{
       "attribute type":"branch label",
       "display order":54
      },
     "EBF site 527 (partition 1)":{
       "attribute type":"branch label",
       "display order":529
      },
     "EBF site 529 (partition 1)":{
       "attribute type":"branch label",
       "display order":531
      },
     "EBF site 537 (partition 1)":{
       "attribute type":"branch label",
       "display order":539
      },
     "EBF site 539 (partition 1)":{
       "attribute type":"branch label",
       "display order":541
      },
     "EBF site 54 (partition 1)":{
       "attribute type":"branch label",
       "display order":56
      },
     "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",
       "display order":562
      },
     "EBF site 564 (partition 1)":{
       "attribute type":"branch label",
       "display order":566
      },
     "EBF site 58 (partition 1)":{
       "attribute type":"branch label",
       "display order":60
      },
     "EBF site 59 (partition 1)":{
       "attribute type":"branch label",
       "display order":61
      },
     "EBF site 60 (partition 1)":{
       "attribute type":"branch label",
       "display order":62
      },
     "EBF site 61 (partition 1)":{
       "attribute type":"branch label",
       "display order":63
      },
     "EBF site 62 (partition 1)":{
       "attribute type":"branch label",
       "display order":64
      },
     "EBF site 64 (partition 1)":{
       "attribute type":"branch label",
       "display order":66
      },
     "EBF site 66 (partition 1)":{
       "attribute type":"branch label",
       "display order":68
      },
     "EBF site 68 (partition 1)":{
       "attribute type":"branch label",
       "display order":70
      },
     "EBF site 69 (partition 1)":{
       "attribute type":"branch label",
       "display order":71
      },
     "EBF site 70 (partition 1)":{
       "attribute type":"branch label",
       "display order":72
      },
     "EBF site 73 (partition 1)":{
       "attribute type":"branch label",
       "display order":75
      },
     "EBF site 77 (partition 1)":{
       "attribute type":"branch label",
       "display order":79
      },
     "EBF site 78 (partition 1)":{
       "attribute type":"branch label",
       "display order":80
      },
     "EBF site 79 (partition 1)":{
       "attribute type":"branch label",
       "display order":81
      },
     "EBF site 8 (partition 1)":{
       "attribute type":"branch label",
       "display order":10
      },
     "EBF site 81 (partition 1)":{
       "attribute type":"branch label",
       "display order":83
      },
     "EBF site 84 (partition 1)":{
       "attribute type":"branch label",
       "display order":86
      },
     "EBF site 86 (partition 1)":{
       "attribute type":"branch label",
       "display order":88
      },
     "EBF site 89 (partition 1)":{
       "attribute type":"branch label",
       "display order":91
      },
     "EBF site 9 (partition 1)":{
       "attribute type":"branch label",
       "display order":11
      },
     "EBF site 99 (partition 1)":{
       "attribute type":"branch label",
       "display order":101
      },
     "Global MG94xREV":{
       "attribute type":"branch length",
       "display order":1
      },
     "Nucleotide GTR":{
       "attribute type":"branch length",
       "display order":0
      },
     "original name":{
       "attribute type":"node label",
       "display order":-1
      }
    }
  },
 "data partitions":{
   "0":{
     "coverage":      [
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 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] 
      ],
     "name":"meme.filter.default"
    }
  },
 "fits":{
   "Global MG94xREV":{
     "AIC-c":7226.087178885974,
     "Equilibrium frequencies":      [
[0.0485984009412611],
      [0.02956900357719973],
      [0.03108082672838122],
      [0.03449710399341214],
      [0.02053762541952889],
      [0.01249582512460089],
      [0.01313471975854296],
      [0.01457843439605254],
      [0.02308459048229354],
      [0.01404548967308914],
      [0.01476361655896873],
      [0.01638637286596178],
      [0.03046946697462319],
      [0.01853871239625653],
      [0.01948657168142254],
      [0.0216284558851606],
      [0.02112660536120122],
      [0.01285418156565452],
      [0.01351139847963371],
      [0.01499651610047861],
      [0.008928077856285582],
      [0.005432161572334556],
      [0.005709900644757894],
      [0.006337509553901212],
      [0.01003528971321133],
      [0.006105828827307119],
      [0.006418011595122538],
      [0.007123453161742795],
      [0.01324562931848419],
      [0.008059114150152886],
      [0.008471165754069981],
      [0.009402281622603544],
      [0.03932718962871962],
      [0.02392806734975356],
      [0.02515147706283166],
      [0.0279160244805243],
      [0.01661962273972026],
      [0.01011197230206122],
      [0.01062898376612524],
      [0.01179727815893297],
      [0.01868069833194261],
      [0.0113660043356041],
      [0.01194713276105585],
      [0.01326031269640911],
      [0.02465674759639369],
      [0.01500204623524711],
      [0.01576908056409512],
      [0.01750235335932507],
      [0.02110645419006403],
      [0.02462414883970813],
      [0.01465982608978509],
      [0.008919561995751803],
      [0.009375607133978042],
      [0.01040613549725428],
      [0.01002571776178019],
      [0.01053831914788704],
      [0.0116966480569341],
      [0.02174920799128454],
      [0.01323299525169244],
      [0.01390958039696969],
      [0.01543846454447198] 
      ],
     "Log Likelihood":-3569.784907463222,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *test*":        [
[0.248895715005128, 1] 
        ]
      },
     "display order":1,
     "estimated parameters":43
    },
   "Nucleotide GTR":{
     "AIC-c":7431.204675852382,
     "Equilibrium frequencies":      [
[0.3476574973769445],
      [0.1861228958532913],
      [0.2296428082660462],
      [0.2365767985037179] 
      ],
     "Log Likelihood":-3679.541894127126,
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0.2089484190839437,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0.1069376934774225,
       "Substitution rate from nucleotide C to nucleotide G":0.01756475048192434,
       "Substitution rate from nucleotide C to nucleotide T":1.483513244796427,
       "Substitution rate from nucleotide G to nucleotide T":0.1186889750817524
      },
     "display order":0,
     "estimated parameters":36
    }
  },
 "input":{
   "file name":"/tmp/tmpu23i1b/job_working_directory/000/3/working/meme_input.fa",
   "number of sequences":13,
   "number of sites":566,
   "partition count":1,
   "trees":{
     "0":"(((((CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516)Node7:0.002095219592954275)Node5:0.003887237703073042)Node4:0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-1,(GOOSE_HONGKONG_W355_97:-1)Node13:0.002899766890966483)Node11:0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716)Node10:0.000182535836694054,HONGKONG_1_538_97:-1)Node9:0.02096173714686362)Node3:0.003130608143291779,(((GOOSE_SHANTOU_2216_2005:0.006207842095177651)Node19:0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232)Node18:0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774)Node17:0.004655295319725731)Node2:0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001)Node25:0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184)Node24:0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072)Node23:0.0004125980823087554,CHICKEN_CK_160_2005:0.006168335080088849)"
    }
  },
 "tested":{
   "0":{
     "CHICKEN_CK_160_2005":"test",
     "CHICKEN_HEBEI_326_2005":"test",
     "CHICKEN_HONGKONG_915_97":"test",
     "CK_HK_WF157_2003":"test",
     "GOOSE_HONGKONG_W355_97":"test",
     "GOOSE_SHANTOU_2216_2005":"test",
     "HONGKONG_1_538_97":"test",
     "HONGKONG_1_97_98":"test",
     "HUMAN_VIETNAM_3062_2004":"test",
     "HUMAN_VIETNAM_CL105_2005":"test",
     "MALLARD_VIETNAM_16_2003":"test",
     "Node10":"test",
     "Node11":"test",
     "Node13":"test",
     "Node17":"test",
     "Node18":"test",
     "Node19":"test",
     "Node2":"test",
     "Node23":"test",
     "Node24":"test",
     "Node25":"test",
     "Node3":"test",
     "Node4":"test",
     "Node5":"test",
     "Node7":"test",
     "Node9":"test",
     "PEREGRINEFALCON_HK_D0028_2004":"test",
     "SWINE_ANHUI_1_2004":"test"
    }
  },
 "timers":{
   "MEME analysis":{
     "order":2,
     "timer":249
    },
   "Model fitting":{
     "order":1,
     "timer":2
    },
   "Total time":{
     "order":0,
     "timer":252
    }
  }
}