{
 "analysis":{
   "info":"FEL (Fixed Effects Likelihood)\n    estimates site-wise synonymous (α) and non-synonymous (β) rates, and\n    uses a likelihood ratio test to determine if beta &neq; alpha at a site.\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, in which case an additional (nuisance) parameter will be\n    inferred -- the non-synonymous rate on branches NOT selected for testing.\n    Multiple partitions within a NEXUS file are also supported\n    for recombination - aware analysis.\n    ",
   "version":"2.00",
   "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",
   "authors":"Sergei L Kosakovsky Pond and Simon DW Frost",
   "contact":"spond@temple.edu",
   "requirements":"in-frame codon alignment and a phylogenetic tree"
  },
 "input":{
   "file name":"/Users/stephenshank/Documents/Data/Datamonkey/CD2.fasta",
   "number of sequences":10,
   "number of sites":187,
   "partition count":1,
   "trees":{
     "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.085099,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"
    }
  },
 "fits":{
   "Nucleotide GTR":{
     "Log Likelihood":-3531.963798530155,
     "estimated parameters":24,
     "AIC-c":7112.142458295762,
     "Equilibrium frequencies":[
      [0.3563279857397504],
      [0.1837789661319073],
      [0.2402852049910873],
      [0.2196078431372549]
      ],
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0.5474490057204714,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0.2645352969683238,
       "Substitution rate from nucleotide C to nucleotide G":0.4863078374555331,
       "Substitution rate from nucleotide C to nucleotide T":1.018028772244997,
       "Substitution rate from nucleotide G to nucleotide T":0.3025951149895378
      },
     "display order":0
    },
   "Global MG94xREV":{
     "Log Likelihood":-3466.725508616141,
     "estimated parameters":31,
     "AIC-c":6996.530451399855,
     "Equilibrium frequencies":[
      [0.04785168648208005],
      [0.03911346079312019],
      [0.04842054060317301],
      [0.04069665666515385],
      [0.01817010744778396],
      [0.01485205303123071],
      [0.01838611113045968],
      [0.01545321970309948],
      [0.0190138898893362],
      [0.01554175184587827],
      [0.01923992433904378],
      [0.01617083546230154],
      [0.02796925133965702],
      [0.02286176927319543],
      [0.02830174586718859],
      [0.02378714529482007],
      [0.01687870337957799],
      [0.01379647304851128],
      [0.01707935503225849],
      [0.01435491300079667],
      [0.006409133648843443],
      [0.005238757839512795],
      [0.006485324528555602],
      [0.005450807083377185],
      [0.006706760641638982],
      [0.005482034985409045],
      [0.006786489669196017],
      [0.005703931360295163],
      [0.009865581170012171],
      [0.008064021368173151],
      [0.009982861811889655],
      [0.008390428826966174],
      [0.03287895020631181],
      [0.02687490503171972],
      [0.033269810543681],
      [0.0279627207822247],
      [0.01248470225271473],
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      [0.01263311863778268],
      [0.01061792547971484],
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      [0.01321977470017749],
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      [0.01921770557551369],
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      [0.01634417558076203],
      [0.01975257768318274],
      [0.02055210293142003],
      [0.009176034326710849],
      [0.007500393094996483],
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      [0.01412467213650941],
      [0.01154535713247913],
      [0.01429258425298098],
      [0.01201267864744234]
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     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *test*":[
        [0.9970623081401093, 1]
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      },
     "display order":1
    }
  },
 "timers":{
   "Total time":{
     "timer":240,
     "order":0
    },
   "Model fitting":{
     "timer":21,
     "order":1
    },
   "FEL analysis":{
     "timer":208,
     "order":2
    }
  },
 "tested":{
   "0":{
     "Pig":"test",
     "Cow":"test",
     "Node3":"test",
     "Horse":"test",
     "Cat":"test",
     "Node2":"test",
     "RhMonkey":"test",
     "Baboon":"test",
     "Node9":"test",
     "Human":"test",
     "Chimp":"test",
     "Node12":"test",
     "Node8":"test",
     "Node1":"test",
     "Rat":"test",
     "Mouse":"test"
    }
  },
 "data partitions":{
   "0":{
     "name":"fel.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]
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    }
  },
 "branch attributes":{
   "0":{
     "Human":{
       "original name":"Human",
       "Nucleotide GTR":0,
       "Global MG94xREV":0
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     "Chimp":{
       "original name":"Chimp",
       "Nucleotide GTR":0.001818647577470898,
       "Global MG94xREV":0.001828142895085465
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       "Nucleotide GTR":0.001683434956773037,
       "Global MG94xREV":0.001771624553208579
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     "RhMonkey":{
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       "Global MG94xREV":0.003717699096857038
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     "Cow":{
       "original name":"Cow",
       "Nucleotide GTR":0.2483322373763571,
       "Global MG94xREV":0.2480141631033857
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     "Pig":{
       "original name":"Pig",
       "Nucleotide GTR":0.187244836750842,
       "Global MG94xREV":0.1926081878751187
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     "Horse":{
       "original name":"Horse",
       "Nucleotide GTR":0.2091766851769093,
       "Global MG94xREV":0.2111575880588217
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     "Cat":{
       "original name":"Cat",
       "Nucleotide GTR":0.266381043956941,
       "Global MG94xREV":0.273601177885004
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     "Mouse":{
       "original name":"Mouse",
       "Nucleotide GTR":0.1181831744338598,
       "Global MG94xREV":0.1201847378516324
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     "Rat":{
       "original name":"Rat",
       "Nucleotide GTR":0.06669700444436912,
       "Global MG94xREV":0.0670850471739789
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     "Node1":{
       "Nucleotide GTR":0.276880831396131,
       "Global MG94xREV":0.2843521449765504
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     "Node12":{
       "Nucleotide GTR":0.01783434870161725,
       "Global MG94xREV":0.01788794906051452
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     "Node2":{
       "Nucleotide GTR":0.06617535490721377,
       "Global MG94xREV":0.06447679597474805
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     "Node3":{
       "Nucleotide GTR":0.09884524766349881,
       "Global MG94xREV":0.1017497956116402
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     "Node8":{
       "Nucleotide GTR":0.1061610073141143,
       "Global MG94xREV":0.1093806684969149
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     "Node9":{
       "Nucleotide GTR":0.02568007351415409,
       "Global MG94xREV":0.02593963430985144
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    },
   "attributes":{
     "original name":{
       "attribute type":"node label",
       "display order":-1
      },
     "Nucleotide GTR":{
       "attribute type":"branch length",
       "display order":0
      },
     "Global MG94xREV":{
       "attribute type":"branch length",
       "display order":1
      }
    }
  },
 "MLE":{
   "headers":[
    ["alpha", "Synonymous substitution rate at a site"],
    ["beta", "Non-synonymous substitution rate at a site"],
    ["alpha=beta", "The rate estimate under the neutral model"],
    ["LRT", "Likelihood ration test statistic for beta = alpha, versus beta &neq; alpha"],
    ["p-value", "Likelihood ration test statistic for beta = alpha, versus beta &neq; alpha"],
    ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
    ],
   "content":{
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