annotate test-data/slac-out1.json @ 17:0b58ef9e84b2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6cabbd9eb2eea9f5d44fe9836cc5f6d6087a839"

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          [0.918128613830821, 2.081871386169179, 0, 2, 0.3060428712769403, 0, 0.9606741383194523, 0.5568190449137107, 0.4815764965055533, 1, 1.725289655759397],
          [0.5100975226897894, 2.436862688713398, 0, 4, 0.1730927756391077, 0, 1.64145481751042, 0.9514082531190525, 0.4675490133082674, 1, 1.725289655759397],
          [0.8966968578847342, 1.637530241370116, 1, 4, 0.3538344523852633, 1.115204086204733, 2.442702979734417, 0.7694353751546591, 0.4210688108565674, 0.887353165393325, 1.725289655759397],
          [0.5446996599261835, 2.444824668946187, 2, 6, 0.1822027854617396, 3.671748207573758, 2.454163718245787, -0.7057275775481558, 0.8347103828697555, 0.4433517293206097, 1.725289655759397],
          [0.9393647524582979, 2.049986259102873, 2, 4, 0.314237019615746, 2.129098409074901, 1.95123259106649, -0.103093308079983, 0.7175136294201356, 0.6100548468646573, 1.725289655759397],
          [0.9971754713302217, 1.65845388744669, 2, 6, 0.3754949718546135, 2.005665058459592, 3.61782745086596, 0.934429988045552, 0.368620599922005, 0.865576719285682, 1.725289655759397],
          [0.4642011124998625, 2.535798887500138, 1, 1, 0.1547337041666208, 2.154238697565155, 0.3943530399549264, -1.020052286139514, 0.9760574807948768, 0.2855248891281182, 1.725289655759397],
          [0.6749720260888831, 2.190994286795493, 0, 1, 0.235512895966169, 0, 0.4564137871224581, 0.2645432815289006, 0.764487104033831, 1, 1.725289655759397],
          [0.4261493864669901, 2.217213369077633, 2, 0, 0.1612148713123518, 4.693189908311464, 0, -2.720233030230351, 1, 0.02599023473225814, 1.725289655759397],
          [0.9324770623328013, 2.040339301342621, 2, 4, 0.3136678988068874, 2.144824876438837, 1.960458242101129, -0.106861264554767, 0.7186004203288798, 0.6088674213175868, 1.725289655759397],
          [1, 2, 4, 0, 0.3333333333333333, 3.999999999999999, 0, -2.31845127375981, 1, 0.01234567901234551, 1.725289655759397],
          [0.7715124115435588, 2.214818162086479, 2.5, 6.5, 0.2583479599868095, 3.24038857002737, 2.934778173336202, -0.1771357033707199, 0.6978100646995695, 0.570992193370048, 1.725289655759397],
          [0.4161749436720388, 2.583825056327961, 0, 0, 0.1387249812240129, 0, 0, 0, 1, 1, 1.725289655759397],
          [0.6547057169104188, 2.274215377615127, 2.5, 5.5, 0.2235313604501436, 3.818509500417371, 2.418416502735822, -0.8115118484642453, 0.8312930612311302, 0.4102750830236512, 1.725289655759397],
          [1, 2, 0, 1, 0.3333333333333333, 0, 0.4999999999999999, 0.2898064092199763, 0.6666666666666667, 1, 1.725289655759397],
          [0.459387925258634, 2.540612074741367, 1, 2, 0.1531293084195446, 2.176809500243183, 0.7872118769661437, -0.8054285949250646, 0.9368355759475114, 0.3926328355868177, 1.725289655759397],
          [0.68260572574677, 2.182710391950512, 0, 5, 0.2382305119950771, 0, 2.290729919296304, 1.327736424808056, 0.2565180128752359, 1, 1.725289655759397],
          [0.6209312921230391, 2.232793122341521, 1, 2, 0.2175862844273782, 1.610484143230854, 0.895739054365506, -0.414275415423359, 0.8785713457104332, 0.5210288393809832, 1.725289655759397],
          [0.7613291257672525, 2.236290545804862, 1, 4, 0.2539778921880274, 1.31349237295003, 1.788676345076781, 0.2754227213618783, 0.6244221032510872, 0.7689220594531727, 1.725289655759397],
          [0.5856189707051693, 2.386950798284423, 0, 6, 0.1970076453089366, 0, 2.513667229467984, 1.456953747492086, 0.2680824983759217, 1, 1.725289655759397],
          [0.203181127576837, 2.790309709539656, 1, 6, 0.06787431084056803, 4.92171695238688, 2.150298936167153, -1.606349407456378, 0.9230321845151072, 0.3886057635842186, 1.725289655759397],
          [0.7145233834068655, 2.170085079520931, 1, 3, 0.2477020339466259, 1.399534323470248, 1.382434277951112, -0.00991140557879772, 0.7421530662286838, 0.6796980736658558, 1.725289655759397],
          [0.8025307113169092, 2.197469288683092, 1, 6, 0.2675102371056363, 1.246058232910557, 2.730413585709635, 0.860351389602304, 0.4023716041625731, 0.8868613698058293, 1.725289655759397],
          [0.886960160336796, 2.113039839663204, 1, 3, 0.295653386778932, 1.127446355223306, 1.419755531196311, 0.1694261453415733, 0.6593591282402262, 0.7538806708089124, 1.725289655759397],
          [0.584073471867688, 2.415926528132312, 1.5, 5.5, 0.1946911572892293, 2.568170054365694, 2.27655929762562, -0.1690213326015218, 0.726177064760956, 0.5944855849772498, 1.725289655759397],
          [0.5268550139960962, 2.205618688973626, 0, 0, 0.1928124737023075, 0, 0, 0, 1, 1, 1.725289655759397],
          [1, 1.954150177116668, 1, 3, 0.3385068260057204, 0.9999999999999998, 1.535194190871489, 0.3102054133837139, 0.5833958240116991, 0.8085296778030449, 1.725289655759397],
          [0.7013114701420603, 2.186058834646365, 0, 2, 0.2428893408576666, 0, 0.9148884596802432, 0.5302810786734529, 0.5732165501869386, 1, 1.725289655759397],
          [0.6103766338418385, 2.230395005807139, 1, 2, 0.2148629707938298, 1.638332702393587, 0.8967021513197104, -0.4298585739491048, 0.8813404805118064, 0.5160100083098675, 1.725289655759397],
          [1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 1.725289655759397],
          [1.416174943672039, 1.583825056327962, 0, 0, 0.4720583145573461, 0, 0, 0, 1, 1, 1.725289655759397],
          [0.566048512190645, 2.433951487809356, 2, 3, 0.1886828373968816, 3.533266066295039, 1.232563596696871, -1.333516642795554, 0.9504034442939914, 0.2397204872545077, 1.725289655759397] 
          ]
        }
      }
    },
   "headers":    [
["ES", "Expected synonymous sites"],
    ["EN", "Expected non-synonymous sites"],
    ["S", "Inferred synonymous substitutions"],
    ["N", "Inferred non-synonymous substitutions"],
    ["P[S]", "Expected proportion of synonymous sites"],
    ["dS", "Inferred synonymous susbsitution rate"],
    ["dN", "Inferred non-synonymous susbsitution rate"],
    ["dN-dS", "Scaled by the length of the tested branches"],
    ["P [dN/dS > 1]", "Binomial probability that S is no greater than the observed value, with P<sub>s</sub> probability of success"],
    ["P [dN/dS < 1]", "Binomial probability that S is no less than the observed value, with P<sub>s</sub> probability of success"],
    ["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 and Simon DW Frost",
   "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222",
   "contact":"[e-mail]",
   "info":"SLAC (Single Likelihood Ancestor Counting)\n    uses a maximum likelihood ancestral state reconstruction\n    and minimum path substitution counting to estimate site - level\n    dS and dN,\n    and applies a simple binomial - based test to test\n    if dS differs drom dN.\n    The estimates aggregate information over all branches,\n    so the signal is derived from\n    pervasive diversification or conservation. A subset of branches can be selected\n    for testing as well.\n    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":"2.00"
  },
 "branch attributes":{
   "0":{
     "Baboon":{
       "Global MG94xREV":0.001710698008755675,
       "Nucleotide GTR":0.001679501710016974,
       "amino-acid":        [
["K", "E", "I", "R", "N", "A", "L", "E", "T", "W", "G", "A", "L", "G", "Q", "D", "I", "D", "L", "D", "I", "P", "S", "F", "Q", "M", "S", "D", "D", "I", "D", "D", "I", "K", "W", "E", "K", "T", "S", "D", "K", "K", "K", "I", "A", "Q", "F", "R", "K", "E", "K", "E", "T", "F", "E", "E", "K", "D", "A", "Y", "K", "L", "F", "K", "N", "G", "T", "L", "K", "I", "K", "H", "-", "L", "K", "I", "H", "D", "Q", "D", "S", "Y", "K", "V", "S", "I", "Y", "D", "T", "K", "G", "K", "N", "V", "L", "E", "K", "T", "F", "D", "L", "K", "I", "Q", "E", "R", "V", "S", "E", "P", "K", "I", "S", "W", "T", "C", "I", "N", "T", "T", "L", "T", "C", "E", "V", "M", "N", "G", "T", "D", "P", "E", "L", "N", "L", "Y", "Q", "D", "G", "K", "H", "L", "K", "-", "L", "S", "Q", "R", "V", "I", "T", "H", "K", "W", "T", "T", "S", "L", "S", "A", "K", "F", "K", "C", "T", "A", "G", "N", "K", "V", "S", "K", "E", "S", "R", "M", "E", "T", "V", "S", "C", "P", "E", "K", "G", "L", "D"] 
        ],
       "codon":        [
["AAA", "GAG", "ATT", "AGG", "AAT", "GCT", "TTG", "GAA", "ACC", "TGG", "GGA", "GCG", "CTG", "GGT", "CAG", "GAC", "ATC", "GAC", "TTG", "GAC", "ATT", "CCT", "AGT", "TTT", "CAA", "ATG", "AGT", "GAT", "GAT", "ATT", "GAT", "GAT", "ATA", "AAA", "TGG", "GAG", "AAA", "ACT", "TCA", "GAC", "AAG", "AAA", "AAG", "ATT", "GCA", "CAA", "TTC", "AGA", "AAA", "GAG", "AAG", "GAG", "ACT", "TTC", "GAG", "GAA", "AAA", "GAT", "GCA", "TAT", "AAG", "CTA", "TTT", "AAA", "AAC", "GGA", "ACT", "CTG", "AAA", "ATT", "AAG", "CAT", "---", "CTG", "AAG", "ATC", "CAT", "GAT", "CAG", "GAT", "AGC", "TAC", "AAG", "GTA", "TCA", "ATA", "TAC", "GAT", "ACA", "AAA", "GGA", "AAA", "AAT", "GTG", "TTG", "GAA", "AAA", "ACA", "TTT", "GAT", "TTG", "AAG", "ATT", "CAA", "GAG", "AGG", "GTC", "TCA", "GAA", "CCA", "AAG", "ATC", "TCC", "TGG", "ACT", "TGT", "ATC", "AAC", "ACA", "ACC", "CTG", "ACC", "TGT", "GAA", "GTA", "ATG", "AAT", "GGA", "ACT", "GAC", "CCC", "GAA", "TTA", "AAC", "CTG", "TAT", "CAA", "GAT", "GGG", "AAA", "CAT", "CTA", "AAA", "---", "CTT", "TCT", "CAG", "AGG", "GTC", "ATC", "ACA", "CAC", "AAG", "TGG", "ACC", "ACC", "AGC", "CTG", "AGT", "GCG", "AAA", "TTC", "AAG", "TGC", "ACA", "GCA", "GGG", "AAC", "AAA", "GTC", "AGC", "AAG", "GAA", "TCC", "AGG", "ATG", "GAG", "ACT", "GTC", "AGC", "TGT", "CCA", "GAG", "AAA", "GGT", "CTG", "GAC"] 
        ],
       "nonsynonymous substitution count":        [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 
        ],
       "original name":"Baboon",
       "synonymous substitution count":        [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 
        ]
      },
     "Cat":{
       "Global MG94xREV":0.270986057489719,
       "Nucleotide GTR":0.2660443541848668,
       "amino-acid":        [
["-", "-", "-", "A", "N", "D", "D", "I", "V", "W", "G", "T", "L", "G", "Q", "D", "I", "N", "L", "D", "I", "P", "D", "S", "Q", "-", "G", "I", "N", "I", "D", "D", "I", "H", "W", "E", "K", "-", "-", "G", "K", "K", "K", "V", "A", "R", "F", "Q", "I", "S", "N", "K", "P", "K", "N", "P", "D", "E", "K", "Y", "N", "V", "S", "M", "N", "G", "T", "L", "K", "I", "K", "H", "-", "L", "M", "L", "E", "D", "C", "D", "T", "Y", "K", "V", "V", "I", "Y", "D", "K", "D", "G", "K", "N", "V", "L", "D", "K", "T", "F", "Q", "L", "K", "I", "Q", "E", "K", "V", "S", "T", "P", "N", "I", "D", "W", "N", "C", "I", "N", "K", "T", "L", "V", "C", "K", "V", "S", "N", "G", "T", "D", "P", "E", "L", "K", "L", "Y", "V", "N", "G", "T", "S", "I", "K", "P", "V", "S", "S", "K", "F", "S", "T", "Y", "R", "F", "I", "N", "K", "Q", "K", "I", "L", "V", "N", "C", "T", "A", "E", "N", "K", "V", "S", "K", "E", "S", "D", "V", "K", "M", "I", "T", "C", "S", "E", "K", "G", "L", "D"] 
        ],
       "codon":        [
["---", "---", "---", "GCA", "AAT", "GAT", "GAT", "ATC", "GTC", "TGG", "GGT", "ACC", "CTG", "GGT", "CAG", "GAC", "ATC", "AAC", "CTG", "GAC", "ATT", "CCT", "GAT", "TCT", "CAA", "---", "GGG", "ATT", "AAT", "ATA", "GAT", "GAT", "ATA", "CAC", "TGG", "GAA", "AAA", "---", "---", "GGC", "AAG", "AAG", "AAG", "GTG", "GCG", "AGG", "TTC", "CAA", "ATT", "AGC", "AAC", "AAG", "CCT", "AAG", "AAT", "CCA", "GAT", "GAA", "AAA", "TAT", "AAT", "GTG", "TCA", "ATG", "AAT", "GGA", "ACT", "CTG", "AAA", "ATT", "AAA", "CAT", "---", "CTG", "ATG", "CTA", "GAA", "GAC", "TGC", "GAT", "ACC", "TAC", "AAG", "GTT", "GTT", "ATA", "TAC", "GAT", "AAG", "GAT", "GGA", "AAG", "AAT", "GTG", "TTG", "GAT", "AAA", "ACA", "TTT", "CAG", "CTG", "AAG", "ATT", "CAA", "GAG", "AAG", "GTC", "TCA", "ACG", "CCT", "AAC", "ATC", "GAC", "TGG", "AAT", "TGT", "ATC", "AAC", "AAA", "ACC", "CTG", "GTC", "TGT", "AAG", "GTA", "TCA", "AAT", "GGA", "ACA", "GAC", "CCT", "GAA", "TTA", "AAA", "CTG", "TAC", "GTA", "AAT", "GGG", "ACC", "AGT", "ATC", "AAG", "CCC", "GTT", "TCT", "TCG", "AAG", "TTC", "AGC", "ACA", "TAC", "AGG", "TTT", "ATA", "AAC", "AAG", "CAG", "AAG", "ATA", "TTA", "GTC", "AAC", "TGC", "ACG", "GCA", "GAA", "AAC", "AAA", "GTC", "AGC", "AAG", "GAA", "AGC", "GAC", "GTG", "AAG", "ATG", "ATC", "ACT", "TGT", "TCA", "GAG", "AAG", "GGT", "CTG", "GAC"] 
        ],
       "nonsynonymous substitution count":        [
[0, 0, 0, 1, 0, 1, 1.5, 2, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1.5, 2, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1.5, 0, 1.5, 0, 1, 1.5, 2, 1, 0, 0, 3, 1, 2, 2, 0, 1, 0, 1, 0, 1, 1.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1.5, 1, 0, 1.5, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 2, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 2, 0, 1, 0, 1, 0, 1, 0, 0, 2, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1.5, 1, 1, 2, 0, 1, 1, 0, 0, 1, 2, 1, 1, 1, 1, 2, 2, 1, 1, 1, 0, 0, 0, 1.5, 0, 0, 0, 0, 0, 0, 0, 2, 1, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0] 
        ],
       "original name":"Cat",
       "synonymous substitution count":        [
[0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0.5, 1, 1.5, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 0, 1, 0.5, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0] 
        ]
      },
     "Chimp":{
       "Global MG94xREV":0.001852173963769908,
       "Nucleotide GTR":0.001818397708700883,
       "amino-acid":        [
["E", "E", "I", "T", "N", "A", "L", "E", "T", "W", "G", "A", "L", "G", "Q", "D", "I", "N", "L", "D", "I", "P", "S", "F", "Q", "M", "S", "D", "D", "I", "D", "D", "I", "K", "W", "E", "K", "T", "S", "D", "K", "K", "K", "I", "A", "Q", "F", "R", "K", "E", "K", "E", "T", "F", "K", "E", "K", "D", "T", "Y", "K", "L", "F", "K", "N", "G", "T", "L", "K", "I", "K", "H", "-", "L", "K", "T", "D", "D", "Q", "D", "I", "Y", "K", "V", "S", "I", "Y", "D", "T", "K", "G", "K", "N", "V", "L", "E", "K", "I", "F", "D", "L", "K", "I", "Q", "E", "R", "V", "S", "K", "P", "K", "I", "S", "W", "T", "C", "I", "N", "T", "T", "L", "T", "C", "E", "V", "M", "N", "G", "T", "D", "P", "E", "L", "N", "L", "Y", "Q", "D", "G", "K", "H", "L", "K", "-", "L", "S", "Q", "R", "V", "I", "T", "H", "K", "W", "T", "T", "S", "L", "S", "A", "K", "F", "K", "C", "T", "A", "G", "N", "K", "V", "S", "K", "E", "S", "S", "V", "E", "P", "V", "S", "C", "P", "E", "K", "G", "L", "D"] 
        ],
       "codon":        [
["GAA", "GAG", "ATT", "ACG", "AAT", "GCC", "TTG", "GAA", "ACC", "TGG", "GGT", "GCC", "TTG", "GGT", "CAG", "GAC", "ATC", "AAC", "TTG", "GAC", "ATT", "CCT", "AGT", "TTT", "CAA", "ATG", "AGT", "GAT", "GAT", "ATT", "GAC", "GAT", "ATA", "AAA", "TGG", "GAA", "AAA", "ACT", "TCA", "GAC", "AAG", "AAA", "AAG", "ATT", "GCA", "CAA", "TTC", "AGA", "AAA", "GAG", "AAA", "GAG", "ACT", "TTC", "AAG", "GAA", "AAA", "GAT", "ACA", "TAT", "AAG", "CTA", "TTT", "AAA", "AAT", "GGA", "ACT", "CTG", "AAA", "ATT", "AAG", "CAT", "---", "CTG", "AAG", "ACC", "GAT", "GAT", "CAG", "GAT", "ATC", "TAC", "AAG", "GTA", "TCA", "ATA", "TAT", "GAT", "ACA", "AAA", "GGA", "AAA", "AAT", "GTG", "TTG", "GAA", "AAA", "ATA", "TTT", "GAT", "TTG", "AAG", "ATT", "CAA", "GAG", "AGG", "GTC", "TCA", "AAA", "CCA", "AAG", "ATC", "TCC", "TGG", "ACT", "TGT", "ATC", "AAC", "ACA", "ACC", "CTG", "ACC", "TGT", "GAG", "GTA", "ATG", "AAT", "GGA", "ACT", "GAC", "CCC", "GAA", "TTA", "AAC", "CTG", "TAT", "CAA", "GAT", "GGG", "AAA", "CAT", "CTA", "AAA", "---", "CTT", "TCT", "CAG", "AGG", "GTC", "ATC", "ACA", "CAC", "AAG", "TGG", "ACC", "ACC", "AGC", "CTG", "AGT", "GCA", "AAA", "TTC", "AAG", "TGC", "ACA", "GCA", "GGG", "AAC", "AAA", "GTC", "AGC", "AAG", "GAA", "TCC", "AGT", "GTC", "GAG", "CCT", "GTC", "AGC", "TGT", "CCA", "GAG", "AAA", "GGT", "CTG", "GAC"] 
        ],
       "nonsynonymous substitution count":        [
[1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 
        ],
       "original name":"Chimp",
       "synonymous substitution count":        [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 
        ]
      },
     "Cow":{
       "Global MG94xREV":0.2526189686412594,
       "Nucleotide GTR":0.2480122076744146,
       "amino-acid":        [
["-", "-", "-", "-", "E", "S", "I", "V", "V", "W", "G", "A", "L", "D", "H", "D", "L", "N", "L", "D", "I", "P", "G", "F", "P", "R", "S", "D", "I", "V", "A", "D", "I", "K", "W", "N", "R", "-", "-", "N", "K", "N", "K", "I", "A", "R", "I", "K", "K", "D", "M", "P", "L", "H", "N", "E", "M", "D", "K", "Y", "D", "M", "F", "T", "N", "G", "T", "L", "K", "I", "K", "T", "-", "L", "M", "R", "N", "D", "S", "G", "L", "Y", "E", "V", "E", "V", "Y", "D", "S", "N", "G", "V", "N", "L", "L", "S", "K", "K", "F", "D", "L", "K", "I", "Q", "E", "M", "L", "S", "G", "P", "E", "I", "N", "W", "I", "C", "T", "N", "R", "T", "V", "S", "C", "K", "V", "E", "N", "G", "S", "N", "P", "K", "L", "Q", "L", "F", "L", "N", "T", "T", "R", "V", "K", "Q", "D", "H", "G", "K", "L", "I", "T", "Y", "T", "W", "N", "T", "R", "W", "N", "K", "T", "F", "K", "C", "V", "A", "S", "N", "H", "V", "D", "S", "K", "V", "S", "I", "E", "I", "A", "V", "C", "P", "D", "E", "G", "L", "D"] 
        ],
       "codon":        [
["---", "---", "---", "---", "GAA", "AGC", "ATT", "GTC", "GTC", "TGG", "GGT", "GCC", "CTG", "GAT", "CAT", "GAC", "CTC", "AAC", "CTG", "GAC", "ATT", "CCT", "GGT", "TTT", "CCA", "AGA", "AGT", "GAT", "ATA", "GTG", "GCA", "GAT", "ATA", "AAA", "TGG", "AAC", "AGA", "---", "---", "AAC", "AAA", "AAC", "AAG", "ATT", "GCA", "CGA", "ATA", "AAG", "AAA", "GAT", "ATG", "CCA", "CTT", "CAC", "AAT", "GAA", "ATG", "GAC", "AAA", "TAT", "GAT", "ATG", "TTT", "ACA", "AAT", "GGA", "ACT", "CTG", "AAA", "ATT", "AAA", "ACT", "---", "CTG", "ATG", "AGA", "AAC", "GAT", "AGT", "GGT", "CTC", "TAT", "GAG", "GTA", "GAG", "GTT", "TAT", "GAT", "TCA", "AAT", "GGA", "GTA", "AAC", "CTA", "CTG", "AGC", "AAA", "AAA", "TTT", "GAT", "TTG", "AAG", "ATT", "CAA", "GAG", "ATG", "CTC", "TCA", "GGA", "CCT", "GAA", "ATT", "AAC", "TGG", "ATC", "TGT", "ACC", "AAC", "AGA", "ACT", "GTG", "AGC", "TGC", "AAG", "GTA", "GAA", "AAT", "GGA", "AGT", "AAT", "CCT", "AAA", "TTA", "CAA", "CTG", "TTT", "TTA", "AAT", "ACG", "ACC", "CGT", "GTC", "AAA", "CAA", "GAT", "CAT", "GGG", "AAG", "CTC", "ATC", "ACC", "TAC", "ACG", "TGG", "AAC", "ACC", "AGA", "TGG", "AAT", "AAA", "ACA", "TTC", "AAG", "TGC", "GTG", "GCG", "AGT", "AAC", "CAT", "GTC", "GAT", "AGC", "AAA", "GTC", "AGC", "ATA", "GAG", "ATC", "GCC", "GTG", "TGT", "CCA", "GAT", "GAA", "GGT", "CTG", "GAT"] 
        ],
       "nonsynonymous substitution count":        [
[0, 0, 0, 0, 2, 1, 1.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1.5, 0, 1.5, 0, 0, 1, 0, 2, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1.5, 0, 0, 0, 1, 2, 1, 0, 0, 0, 1.5, 0, 1, 0, 2, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 1, 0, 1, 0, 1.5, 0, 1, 0, 1, 0, 1.5, 0, 0, 0, 1, 1, 0, 2, 0, 1, 0, 2.833333333333333, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 2, 0, 0, 0, 2, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 2, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 2, 2, 1, 1, 0, 1, 0, 0, 2, 2.5, 0, 0, 1, 1, 0, 0, 0] 
        ],
       "original name":"Cow",
       "synonymous substitution count":        [
[0, 0, 0, 0, 0, 1, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 1, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0.5, 0, 0, 1, 0, 0, 0.5, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0.1666666666666667, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0] 
        ]
      },
     "Horse":{
       "Global MG94xREV":0.2128981270938909,
       "Nucleotide GTR":0.209015715622236,
       "amino-acid":        [
["-", "-", "-", "-", "K", "N", "I", "T", "I", "L", "G", "A", "L", "E", "R", "D", "I", "N", "L", "D", "I", "P", "A", "F", "Q", "M", "S", "E", "H", "V", "E", "D", "I", "Q", "W", "S", "K", "-", "-", "G", "K", "T", "K", "I", "A", "K", "F", "K", "N", "G", "S", "M", "T", "F", "Q", "K", "D", "K", "T", "Y", "E", "V", "L", "K", "N", "G", "T", "L", "K", "I", "K", "H", "-", "L", "E", "R", "I", "H", "E", "G", "T", "Y", "K", "V", "D", "A", "Y", "D", "S", "D", "G", "K", "N", "V", "L", "E", "E", "T", "F", "H", "L", "S", "L", "L", "E", "M", "V", "S", "K", "P", "N", "I", "S", "W", "S", "C", "T", "N", "T", "T", "L", "T", "C", "E", "V", "T", "K", "G", "T", "D", "F", "E", "L", "K", "L", "Y", "L", "N", "G", "R", "M", "I", "Q", "K", "S", "P", "R", "K", "V", "I", "V", "Y", "K", "R", "A", "S", "N", "Q", "I", "A", "S", "F", "K", "C", "T", "A", "N", "N", "T", "V", "S", "E", "E", "S", "S", "S", "V", "V", "I", "R", "C", "T", "E", "K", "G", "L", "D"] 
        ],
       "codon":        [
["---", "---", "---", "---", "AAG", "AAT", "ATC", "ACC", "ATC", "TTG", "GGT", "GCC", "CTG", "GAA", "CGT", "GAT", "ATC", "AAC", "CTG", "GAC", "ATT", "CCT", "GCT", "TTT", "CAA", "ATG", "AGT", "GAG", "CAT", "GTA", "GAA", "GAT", "ATA", "CAA", "TGG", "AGC", "AAA", "---", "---", "GGA", "AAA", "ACC", "AAG", "ATT", "GCA", "AAA", "TTC", "AAA", "AAT", "GGC", "AGT", "ATG", "ACT", "TTC", "CAG", "AAA", "GAT", "AAA", "ACA", "TAC", "GAG", "GTA", "TTA", "AAA", "AAT", "GGA", "ACT", "CTG", "AAA", "ATT", "AAA", "CAT", "---", "CTG", "GAG", "AGA", "ATT", "CAT", "GAA", "GGT", "ACC", "TAC", "AAG", "GTA", "GAC", "GCA", "TAT", "GAT", "AGT", "GAT", "GGA", "AAA", "AAT", "GTG", "TTG", "GAG", "GAA", "ACA", "TTT", "CAT", "TTG", "AGC", "CTT", "CTA", "GAG", "ATG", "GTC", "TCA", "AAA", "CCT", "AAT", "ATC", "TCC", "TGG", "AGC", "TGC", "ACC", "AAC", "ACC", "ACC", "CTG", "ACC", "TGC", "GAG", "GTG", "ACA", "AAA", "GGA", "ACT", "GAC", "TTT", "GAG", "TTA", "AAA", "CTC", "TAT", "CTA", "AAT", "GGG", "AGA", "ATG", "ATC", "CAA", "AAA", "AGT", "CCT", "CGC", "AAA", "GTC", "ATC", "GTA", "TAC", "AAG", "CGG", "GCC", "AGC", "AAC", "CAA", "ATT", "GCG", "TCC", "TTC", "AAG", "TGC", "ACA", "GCC", "AAT", "AAC", "ACA", "GTC", "AGC", "GAG", "GAA", "AGC", "AGC", "TCT", "GTG", "GTC", "ATC", "AGG", "TGT", "ACA", "GAG", "AAA", "GGT", "CTG", "GAT"] 
        ],
       "nonsynonymous substitution count":        [
[0, 0, 0, 0, 1, 0, 1.5, 1, 1, 1, 0, 0, 0, 1.5, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 2.833333333333333, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 1, 2, 1, 1, 0, 1, 1, 2, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 2, 1, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1.5, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 2, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 1, 1, 1, 0, 1.5, 0, 0, 0, 2, 0, 0, 1, 1, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 2, 0, 1, 0, 0, 1, 0, 0, 0, 2.5, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0] 
        ],
       "original name":"Horse",
       "synonymous substitution count":        [
[0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0.5, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.1666666666666667, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] 
        ]
      },
     "Human":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "amino-acid":        [
["K", "E", "I", "T", "N", "A", "L", "E", "T", "W", "G", "A", "L", "G", "Q", "D", "I", "N", "L", "D", "I", "P", "S", "F", "Q", "M", "S", "D", "D", "I", "D", "D", "I", "K", "W", "E", "K", "T", "S", "D", "K", "K", "K", "I", "A", "Q", "F", "R", "K", "E", "K", "E", "T", "F", "K", "E", "K", "D", "T", "Y", "K", "L", "F", "K", "N", "G", "T", "L", "K", "I", "K", "H", "-", "L", "K", "T", "D", "D", "Q", "D", "I", "Y", "K", "V", "S", "I", "Y", "D", "T", "K", "G", "K", "N", "V", "L", "E", "K", "I", "F", "D", "L", "K", "I", "Q", "E", "R", "V", "S", "K", "P", "K", "I", "S", "W", "T", "C", "I", "N", "T", "T", "L", "T", "C", "E", "V", "M", "N", "G", "T", "D", "P", "E", "L", "N", "L", "Y", "Q", "D", "G", "K", "H", "L", "K", "-", "L", "S", "Q", "R", "V", "I", "T", "H", "K", "W", "T", "T", "S", "L", "S", "A", "K", "F", "K", "C", "T", "A", "G", "N", "K", "V", "S", "K", "E", "S", "S", "V", "E", "P", "V", "S", "C", "P", "E", "K", "G", "L", "D"] 
        ],
       "codon":        [
["AAA", "GAG", "ATT", "ACG", "AAT", "GCC", "TTG", "GAA", "ACC", "TGG", "GGT", "GCC", "TTG", "GGT", "CAG", "GAC", "ATC", "AAC", "TTG", "GAC", "ATT", "CCT", "AGT", "TTT", "CAA", "ATG", "AGT", "GAT", "GAT", "ATT", "GAC", "GAT", "ATA", "AAA", "TGG", "GAA", "AAA", "ACT", "TCA", "GAC", "AAG", "AAA", "AAG", "ATT", "GCA", "CAA", "TTC", "AGA", "AAA", "GAG", "AAA", "GAG", "ACT", "TTC", "AAG", "GAA", "AAA", "GAT", "ACA", "TAT", "AAG", "CTA", "TTT", "AAA", "AAT", "GGA", "ACT", "CTG", "AAA", "ATT", "AAG", "CAT", "---", "CTG", "AAG", "ACC", "GAT", "GAT", "CAG", "GAT", "ATC", "TAC", "AAG", "GTA", "TCA", "ATA", "TAT", "GAT", "ACA", "AAA", "GGA", "AAA", "AAT", "GTG", "TTG", "GAA", "AAA", "ATA", "TTT", "GAT", "TTG", "AAG", "ATT", "CAA", "GAG", "AGG", "GTC", "TCA", "AAA", "CCA", "AAG", "ATC", "TCC", "TGG", "ACT", "TGT", "ATC", "AAC", "ACA", "ACC", "CTG", "ACC", "TGT", "GAG", "GTA", "ATG", "AAT", "GGA", "ACT", "GAC", "CCC", "GAA", "TTA", "AAC", "CTG", "TAT", "CAA", "GAT", "GGG", "AAA", "CAT", "CTA", "AAA", "---", "CTT", "TCT", "CAG", "AGG", "GTC", "ATC", "ACA", "CAC", "AAG", "TGG", "ACC", "ACC", "AGC", "CTG", "AGT", "GCA", "AAA", "TTC", "AAG", "TGC", "ACA", "GCA", "GGG", "AAC", "AAA", "GTC", "AGC", "AAG", "GAA", "TCC", "AGT", "GTC", "GAG", "CCT", "GTC", "AGC", "TGT", "CCA", "GAG", "AAA", "GGT", "CTG", "GAC"] 
        ],
       "nonsynonymous substitution count":        [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 
        ],
       "original name":"Human",
       "synonymous substitution count":        [
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        ]
      },
     "Mouse":{
       "Global MG94xREV":0.1202934609265267,
       "Nucleotide GTR":0.1180997886803625,
       "amino-acid":        [
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        ],
       "codon":        [
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        ],
       "nonsynonymous substitution count":        [
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        ],
       "original name":"Mouse",
       "synonymous substitution count":        [
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        ]
      },
     "Node1":{
       "Global MG94xREV":0.28199060274564,
       "Nucleotide GTR":0.2768482204901319,
       "amino-acid":        [
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        ],
       "codon":        [
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        ],
       "nonsynonymous substitution count":        [
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        ],
       "synonymous substitution count":        [
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        ]
      },
     "Node12":{
       "Global MG94xREV":0.01816964082591924,
       "Nucleotide GTR":0.01783829915118819,
       "amino-acid":        [
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        ],
       "codon":        [
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        ],
       "nonsynonymous substitution count":        [
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        ],
       "synonymous substitution count":        [
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        ]
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     "Node16":{
       "amino-acid":        [
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        ],
       "codon":        [
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        ],
       "nonsynonymous substitution count":        [
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       "synonymous substitution count":        [
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       "amino-acid":        [
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       "nonsynonymous substitution count":        [
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       "synonymous substitution count":        [
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       "amino-acid":        [
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       "nonsynonymous substitution count":        [
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       "synonymous substitution count":        [
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       "amino-acid":        [
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       "nonsynonymous substitution count":        [
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       "synonymous substitution count":        [
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       "amino-acid":        [
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        ],
       "codon":        [
["AAA", "GAG", "ATT", "AGG", "AAT", "GCT", "TTG", "GAA", "ACC", "TGG", "GGA", "GCG", "CTG", "GGT", "CAG", "GAC", "ATC", "GAC", "TTG", "GAC", "ATT", "CCT", "AGT", "TTT", "CAA", "ATG", "AGT", "GAT", "GAT", "ATT", "GAT", "GAT", "ATA", "AAA", "TGG", "GAA", "AAA", "ACT", "TCA", "GAC", "AAG", "AAA", "AAG", "ATT", "GCA", "CAA", "TTC", "AGA", "AAA", "GAG", "AAG", "GAG", "ACT", "TTC", "GAG", "GAA", "AAA", "GAT", "GCA", "TAT", "AAG", "CTA", "TTT", "AAA", "AAC", "GGA", "ACT", "CTG", "AAA", "ATT", "AAG", "CAT", "---", "CTG", "AAG", "ATC", "CAT", "GAT", "CAG", "GAT", "AGC", "TAC", "AAG", "GTA", "TCA", "ATA", "TAC", "GAT", "ACA", "AAA", "GGA", "AAA", "AAT", "GTG", "TTG", "GAA", "AAA", "ACA", "TTT", "GAT", "TTG", "AAG", "ATT", "CAA", "GAG", "AGG", "GTC", "TCA", "GAA", "CCA", "AAG", "ATC", "TCC", "TGG", "ACT", "TGT", "ATC", "AAC", "ACA", "ACC", "CTG", "ACC", "TGT", "GAA", "GTA", "ATG", "AAT", "GGA", "ACT", "GAC", "CCC", "GAA", "TTA", "AAC", "CTG", "TAT", "CAA", "GAT", "GGG", "AAA", "CAT", "CTA", "AAA", "---", "CTT", "TCT", "CAG", "AGG", "GTC", "ATC", "ACA", "CAC", "AAG", "TGG", "ACC", "ACC", "AGC", "CTG", "AGT", "GCG", "AAA", "TTC", "AAG", "TGC", "ACA", "GCA", "GGG", "AAC", "AAA", "GTC", "AGC", "AAG", "GAA", "TCC", "AGG", "ATG", "GAG", "ACT", "GTC", "AGC", "TGT", "CCA", "GAG", "AAA", "GGT", "CTG", "GAC"] 
        ],
       "nonsynonymous substitution count":        [
[0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 
        ],
       "synonymous substitution count":        [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 
        ]
      },
     "Pig":{
       "Global MG94xREV":0.190671339253091,
       "Nucleotide GTR":0.1871942556124935,
       "amino-acid":        [
["-", "-", "-", "-", "-", "T", "E", "V", "V", "W", "G", "I", "V", "D", "Q", "D", "I", "N", "L", "D", "I", "P", "E", "L", "S", "K", "H", "D", "N", "V", "D", "H", "I", "R", "W", "Q", "K", "-", "-", "N", "E", "N", "K", "I", "A", "E", "F", "K", "K", "N", "K", "E", "T", "H", "P", "V", "K", "D", "T", "Y", "M", "M", "L", "P", "N", "G", "T", "L", "R", "I", "K", "D", "-", "L", "K", "R", "D", "D", "E", "G", "I", "Y", "K", "V", "T", "V", "Y", "A", "T", "D", "G", "K", "H", "M", "L", "E", "R", "K", "F", "D", "L", "P", "I", "L", "D", "G", "V", "S", "K", "P", "V", "I", "S", "W", "S", "C", "A", "D", "K", "T", "V", "T", "C", "E", "V", "A", "E", "G", "S", "D", "P", "K", "L", "K", "L", "Y", "V", "N", "K", "S", "T", "A", "R", "E", "G", "R", "Q", "K", "V", "I", "L", "W", "K", "W", "N", "T", "K", "W", "S", "T", "L", "F", "K", "C", "V", "A", "S", "N", "N", "A", "S", "E", "Q", "I", "S", "M", "V", "T", "I", "S", "C", "T", "G", "Q", "G", "L", "D"] 
        ],
       "codon":        [
["---", "---", "---", "---", "---", "ACT", "GAG", "GTT", "GTC", "TGG", "GGC", "ATC", "GTG", "GAT", "CAA", "GAC", "ATC", "AAC", "CTG", "GAC", "ATT", "CCT", "GAA", "CTT", "TCA", "AAA", "CAT", "GAT", "AAC", "GTA", "GAT", "CAT", "ATA", "CGA", "TGG", "CAG", "AAG", "---", "---", "AAT", "GAA", "AAC", "AAG", "ATC", "GCA", "GAA", "TTT", "AAA", "AAA", "AAC", "AAA", "GAA", "ACT", "CAC", "CCT", "GTG", "AAA", "GAC", "ACA", "TAC", "ATG", "ATG", "TTA", "CCA", "AAT", "GGA", "ACT", "CTG", "AGA", "ATT", "AAA", "GAT", "---", "CTG", "AAG", "AGA", "GAT", "GAT", "GAG", "GGT", "ATC", "TAC", "AAG", "GTA", "ACT", "GTC", "TAT", "GCT", "ACG", "GAT", "GGA", "AAA", "CAC", "ATG", "CTG", "GAG", "AGA", "AAA", "TTT", "GAT", "TTG", "CCG", "ATT", "CTA", "GAT", "GGG", "GTC", "TCA", "AAA", "CCT", "GTA", "ATC", "TCC", "TGG", "AGC", "TGT", "GCC", "GAC", "AAA", "ACG", "GTG", "ACC", "TGT", "GAG", "GTA", "GCA", "GAA", "GGA", "AGT", "GAC", "CCT", "AAG", "TTA", "AAA", "CTG", "TAT", "GTA", "AAT", "AAG", "TCC", "ACT", "GCC", "AGA", "GAA", "GGT", "CGT", "CAG", "AAG", "GTC", "ATC", "CTG", "TGG", "AAG", "TGG", "AAC", "ACC", "AAA", "TGG", "AGC", "ACA", "TTA", "TTC", "AAG", "TGT", "GTG", "GCC", "AGT", "AAC", "AAC", "GCC", "AGT", "GAG", "CAA", "ATC", "AGC", "ATG", "GTG", "ACC", "ATC", "AGT", "TGT", "ACG", "GGG", "CAA", "GGT", "CTG", "GAT"] 
        ],
       "nonsynonymous substitution count":        [
[0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 2, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 2, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 1, 0, 2, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 2, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 2.166666666666667, 2, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0] 
        ],
       "original name":"Pig",
       "synonymous substitution count":        [
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        ]
      },
     "Rat":{
       "Global MG94xREV":0.06785010407729926,
       "Nucleotide GTR":0.06661278918863184,
       "amino-acid":        [
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        ],
       "codon":        [
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        ],
       "nonsynonymous substitution count":        [
[0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 
        ],
       "original name":"Rat",
       "synonymous substitution count":        [
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        ]
      },
     "RhMonkey":{
       "Global MG94xREV":0.003845100000905624,
       "Nucleotide GTR":0.003774980735147155,
       "amino-acid":        [
["K", "E", "I", "R", "N", "A", "L", "E", "T", "W", "G", "A", "L", "G", "Q", "D", "I", "D", "L", "D", "I", "P", "S", "F", "Q", "M", "S", "D", "D", "I", "D", "D", "I", "R", "W", "E", "K", "T", "S", "D", "K", "K", "K", "I", "A", "Q", "F", "R", "K", "E", "K", "E", "T", "F", "E", "E", "K", "D", "A", "Y", "K", "L", "F", "K", "N", "G", "T", "L", "K", "TI", "K", "H", "-", "L", "K", "I", "H", "D", "Q", "D", "S", "Y", "K", "V", "S", "I", "Y", "D", "T", "K", "G", "K", "N", "V", "L", "E", "K", "T", "F", "D", "L", "K", "I", "Q", "E", "R", "V", "S", "E", "P", "K", "I", "S", "W", "T", "C", "I", "N", "T", "T", "L", "T", "C", "E", "V", "M", "N", "G", "T", "DG", "P", "E", "L", "N", "L", "Y", "Q", "D", "G", "K", "H", "V", "K", "-", "L", "S", "Q", "R", "V", "I", "T", "H", "K", "W", "T", "T", "S", "L", "S", "A", "K", "F", "K", "C", "T", "A", "G", "N", "K", "V", "S", "K", "E", "S", "R", "M", "E", "T", "V", "S", "C", "P", "E", "K", "G", "L", "D"] 
        ],
       "codon":        [
["AAA", "GAG", "ATT", "AGG", "AAT", "GCT", "TTG", "GAA", "ACC", "TGG", "GGA", "GCG", "CTG", "GGT", "CAG", "GAC", "ATC", "GAC", "TTG", "GAC", "ATT", "CCT", "AGT", "TTT", "CAA", "ATG", "AGT", "GAT", "GAT", "ATT", "GAT", "GAT", "ATA", "AGA", "TGG", "GAA", "AAA", "ACT", "TCA", "GAC", "AAG", "AAA", "AAG", "ATT", "GCA", "CAA", "TTC", "AGA", "AAA", "GAG", "AAG", "GAG", "ACT", "TTC", "GAG", "GAA", "AAA", "GAT", "GCA", "TAT", "AAG", "CTA", "TTT", "AAA", "AAC", "GGA", "ACT", "CTG", "AAA", "AYT", "AAG", "CAT", "---", "CTG", "AAG", "ATC", "CAT", "GAT", "CAG", "GAT", "AGC", "TAC", "AAG", "GTA", "TCA", "ATA", "TAC", "GAT", "ACA", "AAA", "GGA", "AAA", "AAT", "GTG", "TTG", "GAA", "AAA", "ACA", "TTT", "GAT", "TTG", "AAG", "ATT", "CAA", "GAG", "AGG", "GTC", "TCA", "GAA", "CCA", "AAG", "ATC", "TCC", "TGG", "ACT", "TGT", "ATC", "AAC", "ACA", "ACC", "CTG", "ACC", "TGT", "GAA", "GTA", "ATG", "AAT", "GGA", "ACT", "GRC", "CCC", "GAA", "TTA", "AAC", "CTG", "TAT", "CAA", "GAT", "GGG", "AAA", "CAT", "GTA", "AAA", "---", "CTT", "TCT", "CAG", "AGG", "GTC", "ATC", "ACA", "CAC", "AAG", "TGG", "ACC", "ACC", "AGC", "CTG", "AGT", "GCG", "AAA", "TTC", "AAG", "TGC", "ACA", "GCA", "GGG", "AAC", "AAA", "GTC", "AGC", "AAG", "GAA", "TCC", "AGG", "ATG", "GAG", "ACT", "GTC", "AGC", "TGT", "CCA", "GAG", "AAA", "GGT", "CTG", "GAC"] 
        ],
       "nonsynonymous substitution count":        [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 
        ],
       "original name":"RhMonkey",
       "synonymous substitution count":        [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 
        ]
      }
    },
   "attributes":{
     "Global MG94xREV":{
       "attribute type":"branch length",
       "display order":1
      },
     "Nucleotide GTR":{
       "attribute type":"branch length",
       "display order":0
      },
     "amino-acid":{
       "attribute type":"node label",
       "display order":1
      },
     "codon":{
       "attribute type":"node label",
       "display order":0
      },
     "nonsynonymous substitution count":{
       "attribute type":"branch label",
       "display order":1
      },
     "original name":{
       "attribute type":"node label",
       "display order":-1
      },
     "synonymous substitution count":{
       "attribute type":"branch label",
       "display order":0
      }
    }
  },
 "data partitions":{
   "0":{
     "coverage":      [
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     "name":"slac.filter.default"
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     "Rate Distributions":{
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       "Substitution rate from nucleotide C to nucleotide T":1.029008842850363,
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     "estimated parameters":24
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   "number of sequences":10,
   "number of sites":187,
   "partition count":1,
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      ]
    }
  },
 "tested":{
   "0":{
     "Baboon":"test",
     "Cat":"test",
     "Chimp":"test",
     "Cow":"test",
     "Horse":"test",
     "Human":"test",
     "Mouse":"test",
     "Node1":"test",
     "Node12":"test",
     "Node2":"test",
     "Node3":"test",
     "Node8":"test",
     "Node9":"test",
     "Pig":"test",
     "Rat":"test",
     "RhMonkey":"test"
    }
  },
 "timers":{
   "Ancestor sampling analysis":{
     "order":3,
     "timer":12
    },
   "Model fitting":{
     "order":1,
     "timer":1
    },
   "Primary SLAC analysis":{
     "order":2,
     "timer":1
    },
   "Total time":{
     "order":0,
     "timer":14
    }
  }
}