view test-data/summary/nsp8.CFEL.json @ 8:4e7f1a7d18be draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954

{
 "MLE":{
   "content":{
     "0":      [
[0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [3.206171473304911, 0, 0.03175555207671071, 5.433962997865532e-05, 0, 0, 0.9766417072604165, 1, -1, 0.1428350861439815],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 2.691597641547223, 0.6095939176926283, 0, 0, 0, 1, 1, -1, 0.334509864610243],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [3.229642435228862, 0, 2.162021710309243, 0.004452160407161729, 0, 0, 0.8693548005974709, 1, -1, 0.1442288861347906],
      [0, 2.170494633509469, 0.2961869984298745, 0, 0, 0, 0.9875062279782896, 1, -1, 0.2697178710749373],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [6.636646908481298, 0, 1.139449512908137, 6.624437421595782e-05, 0, 0, 0.906603671841744, 1, -1, 0.2958257534388632],
      [0, 3.585093121716918, 0.4689445336386987, 0, 0, 0, 1, 1, -1, 0.4455007553375522],
      [6.636646908481298, 0, 1.139449512908137, 6.624437421595782e-05, 0, 0, 0.906603671841744, 1, -1, 0.2958257534388632],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [6.1753737985279, 0, 0.6747812225964546, 0.0008286376705392658, 0, 0, 0.9318895682175306, 1, -1, 0.275210444662231],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 2.525862203077411, 0, 0, 0, 0, 0.9967237889019069, 1, -1, 0.3138254899904328],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 2.732340409070313, 0, 0, 0, 0, 0.9864042469335919, 1, -1, 0.339479353486676],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [6.138037520514744, 0, 0.002569672061179798, 0, 0, 0, 0.966625447399751, 1, -1, 0.2734404264031591],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 2.524146157767697, 0.7467703676904078, 0, 0, 0, 1, 1, -1, 0.3137257081336548],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [20.45569800257852, 2.869360506651708, 0, 0, 0, 0, 0.8631784781924842, 1, -1, 1.267772969506594],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [11.83304129427042, 0, 3030.146710177266, 0, 1, 0, 0.00724053140174763, 1, 0.25, 0.987396913560512],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 3.197005952555818, 0, 0, 0, 0, 0.984992303013053, 1, -1, 0.3972116762113058],
      [15.5072203666105, 0, 0.06830082577521719, 0, 0, 0, 0.9698119015081345, 1, -1, 0.6908329511612732],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 1.96219769621343, 1.575465255150986, 0, 0, 0, 1, 1, -1, 0.2440323508941374],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [6.142239259843736, 0, 0, 0, 0, 0, 0.9658107256738867, 1, -1, 0.2736272170517046],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 1.692063018416472, 0.4337954874831223, 0, 0, 0, 0.9397342242479334, 1, -1, 0.2102960857470568],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0.9922672528050931, 1.686153897880079, 0.02862512334425974, 0, 0, 0, 1, 1, -1, 0.2537043303927004],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [15.49048275885172, 0, 0, 0, 0, 0, 0.9733919429509413, 1, -1, 0.6900769424276455],
      [0, 2.529401737682274, 0.8317478715977954, 0, 0, 0, 1, 1, -1, 0.3143915944746369],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 2.319498114533182, 0.04144050098586084, 0, 0, 0, 0.9928070378879535, 1, -1, 0.2881920994616917],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 5.298353743328299, 0, 0, 0, 0, 0.9918665304379798, 1, -1, 0.6582934166467226],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 2.32993960310445, 0.03925147582932535, 0, 0, 0, 0.9873005963656539, 1, -1, 0.2894890686426316],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 4.238961562619959, 1.383565947837822, 0.0006564755206712942, 0, 0, 1, 1, -1, 0.5268831732477733],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 2.775976834009799, 0.1697290282745423, 0, 0, 0, 0.9671678247668708, 1, -1, 0.3449267370056278],
      [0, 3.723229850445897, 0.2599250657679609, 0, 0, 0, 0.982699093997216, 1, -1, 0.4626317907453247],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 2.857806383268142, 0.8922869626267136, 0, 0, 0, 1, 1, -1, 0.3552033913039622],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [20.37098793536531, 0, 0.6757806667437544, 0, 0, 0, 0.9330728419167265, 1, -1, 0.9075985114615732],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [20.36167794145505, 0, 0.02201254975439628, 0, 0, 0, 0.9770415900084612, 1, -1, 0.9070844639240161],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [3.171188468881345, 0, 0.07771324886221978, 0, 0, 0, 0.9768594429929136, 1, -1, 0.1412833238206972],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [3.192110034483986, 0, 0, 0, 0, 0, 0.9745355561336112, 1, -1, 0.14220354309039],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 3.756232495704726, 0, 0, 0, 0, 0.9895702078955098, 1, -1, 0.4666927206267694],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 2.570479655417568, 0, 0, 0, 0, 0.9842070861815725, 1, -1, 0.3193689807737838],
      [0, 2.534350394398107, 0.01191926342770548, 0, 0, 0, 0.9963088747177953, 1, -1, 0.3148819148831776],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [5.198458685829157, 0, 0.6892659904974067, 0, 0, 1, 0.9180287250150805, 1, -1, 0.2316879522379306],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 2349.955221801233, 0, 1, 0, 0.007496866564663529, 0.7421897899016894, 1, 0.3569380510274729],
      [0, 3.329389173655115, 0.7642144194635947, 0, 0, 0, 1, 1, -1, 0.4137756935381093],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 4.416024379863759, 7.215119897204079, 0.08906090118487382, 0, 0, 1, 1, -1, 0.5502633161942482],
      [3.866154229633559, 0, 0.4098695586777816, 0, 0, 0, 0.9533590573719652, 1, -1, 0.1722934205280044],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 3.738606829771655, 0.1834038883182344, 0, 0, 0, 0.9899383765810306, 1, -1, 0.4645306790514804],
      [0, 3.747072669534603, 0, 0, 0, 0, 0.980095324166522, 1, -1, 0.4655546589650666],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 3.700633988003308, 0, 0, 0, 0, 1, 1, -1, 0.4597848897479206],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [4.096210800342686, 0, 0.6141017336968563, 0, 0, 0, 0.9537842489101511, 1, -1, 0.1825731044764183],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [14.14005853525352, 0, 0, 0, 0, 0, 0.9730315243980995, 1, -1, 0.6299176411516176],
      [0, 2.963989796064166, 0, 0, 0, 0, 1, 1, -1, 0.3682606077810544],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [20.2323553240181, 2.973654321970214, 0, 0, 0, 0, 0.8600279492836433, 1, -1, 1.27078137451203],
      [0, 2.22263423878483, 0, 0, 0, 0, 0.9934951200984368, 1, -1, 0.2761509627113989],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 4.625496763788704, 0.9193082115881646, 0, 0, 0, 1, 1, -1, 0.5748340053685835],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [20.20013218757843, 0, 0.08065987678753951, 0, 0, 0, 0.9689465191088908, 1, -1, 0.8998967595764576],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [20.14713181573507, 0, 1.054064405079435, 0, 0, 0, 0.927134103324357, 1, -1, 0.8976835271493999],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [14.33371046920479, 3.747852458133841, 0.217922169290721, 0, 0, 0, 0.8347955443964278, 1, -1, 1.104229178199352],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 1.889771002615388, 0.5157084554508564, 0, 0, 0, 1, 1, -1, 0.2348727358148539],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],
      [0, 5.651971820557556, 0, 0, 0, 0, 0.9946823441693979, 1, -1, 0.7022286583320135] 
      ]
    },
   "headers":    [
["alpha", "Synonymous substitution rate at a site"],
    ["beta (background)", "Non-synonymous substitution rate at a site for background branches"],
    ["beta (B-1-617)", "Non-synonymous substitution rate at a site for B-1-617 branches"],
    ["beta (Reference)", "Non-synonymous substitution rate at a site for Reference branches"],
    ["subs (B-1-617)", "Substitutions mapped to B-1-617 branches"],
    ["subs (Reference)", "Substitutions mapped to Reference branches"],
    ["P-value (overall)", "P-value for the test that non-synonymous rates differ between any of the selected groups: B-1-617,Reference"],
    ["Q-value (overall)", "Q-value for the test that non-synonymous rates differ between any of the selected groups: B-1-617,Reference"],
    ["Permutation p-value", "Label permutation test for significant sites"],
    ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale beta-alpha"] 
    ]
  },
 "analysis":{
   "authors":"Sergei L Kosakovsky Pond and Steven Weaver",
   "citation":"TBD",
   "contact":"[e-mail]",
   "help":"http://www.hyphy.org/methods/other/contrast-fel/",
   "info":"Contrast-FEL (Fixed Effects Likelihood) investigates whether or not selective pressures differ between two or more sets of\n    branches at a site. Site-specific synonymous (alpha) and non-synonymous (beta, one per branch set) substitution rates are estimated\n    and then beta rates are tested for equality at each site. LRT and permutation tests ar used to assess significance at each site, and FDR is applied alignment wide to call sites with different selective profiles",
   "requirements":"in-frame codon alignment and a phylogenetic tree; only single partition data are supported",
   "version":"0.5"
  },
 "branch attributes":{
   "0":{
     "Node20":{
       "Global MG94xREV":0.001634892186392535,
       "Nucleotide GTR":0.001684521619549293
      },
     "Node38":{
       "Global MG94xREV":0.001919664151147453,
       "Nucleotide GTR":0.00168484920326581
      },
     "Node4":{
       "Global MG94xREV":0.001634608725470079,
       "Nucleotide GTR":0.001683801387489096
      },
     "REFERENCE":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"REFERENCE"
      },
     "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021"
      },
     "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{
       "Global MG94xREV":0.001728428286527107,
       "Nucleotide GTR":0.001682745450340891,
       "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021"
      },
     "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021"
      },
     "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{
       "Global MG94xREV":0.001727412680411063,
       "Nucleotide GTR":0.00168274558227101,
       "original name":"epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021"
      },
     "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":{
       "Global MG94xREV":0.001731169192232254,
       "Nucleotide GTR":0.001684401404203384,
       "original name":"epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021"
      },
     "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{
       "Global MG94xREV":0.001728394297110263,
       "Nucleotide GTR":0.00168406792173386,
       "original name":"epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021"
      },
     "epi_isl_1543980_hCoV_19_Singapore_490_2021":{
       "Global MG94xREV":0.001731480337658913,
       "Nucleotide GTR":0.001684975469042935,
       "original name":"epi_isl_1543980/hCoV-19/Singapore/490/2021"
      },
     "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":{
       "Global MG94xREV":0.00173257034392943,
       "Nucleotide GTR":0.001684401583391051,
       "original name":"epi_isl_1544068/hCoV-19/India/MH-NCCS-RT231527/2021"
      },
     "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":{
       "Global MG94xREV":0.001728428527066194,
       "Nucleotide GTR":0.001682745512695379,
       "original name":"epi_isl_1573247/hCoV-19/Germany/un-RKI-I-068985/2021"
      },
     "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021"
      },
     "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":{
       "Global MG94xREV":0.001730278969738805,
       "Nucleotide GTR":0.001684431017860219,
       "original name":"epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021"
      },
     "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":{
       "Global MG94xREV":0.00173028305819776,
       "Nucleotide GTR":0.001684439221071522,
       "original name":"epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021"
      },
     "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"epi_isl_1615709/hCoV-19/England/CAMC-14E792B/2021"
      },
     "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":{
       "Global MG94xREV":0.001732590473818113,
       "Nucleotide GTR":0.00168443927661716,
       "original name":"epi_isl_1632256/hCoV-19/England/RAND-14E1D70/2021"
      },
     "epi_isl_1652105_hCoV_19_Singapore_561_2021":{
       "Global MG94xREV":0.001730912440099921,
       "Nucleotide GTR":0.001685171120971631,
       "original name":"epi_isl_1652105/hCoV-19/Singapore/561/2021"
      },
     "epi_isl_1652118_hCoV_19_Singapore_575_2021":{
       "Global MG94xREV":0.00173012682288667,
       "Nucleotide GTR":0.001684401899924961,
       "original name":"epi_isl_1652118/hCoV-19/Singapore/575/2021"
      },
     "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":{
       "Global MG94xREV":0.01048097604892967,
       "Nucleotide GTR":0.01020457779555702,
       "original name":"gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human"
      },
     "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.02680857534231693,
       "Nucleotide GTR":0.02592331511084145,
       "original name":"gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human"
      },
     "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.005248107108130198,
       "Nucleotide GTR":0.005093980037543817,
       "original name":"gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human"
      },
     "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.003471698044100598,
       "Nucleotide GTR":0.003379296026417724,
       "original name":"gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human"
      },
     "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.003457568777482139,
       "Nucleotide GTR":0.003372774424630234,
       "original name":"gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human"
      },
     "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.003467133892779525,
       "Nucleotide GTR":0.003374190595560375,
       "original name":"gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human"
      },
     "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.005201716586138184,
       "Nucleotide GTR":0.00505933790460295,
       "original name":"gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human"
      },
     "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":{
       "Global MG94xREV":0.003459439643420186,
       "Nucleotide GTR":0.003373764235314068,
       "original name":"gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human"
      },
     "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":{
       "Global MG94xREV":0.005223283115211614,
       "Nucleotide GTR":0.005068409188375663,
       "original name":"gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human"
      },
     "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.003458770062029164,
       "Nucleotide GTR":0.003372774424770855,
       "original name":"gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human"
      },
     "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.001732985724599283,
       "Nucleotide GTR":0.001686266012390882,
       "original name":"gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human"
      },
     "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":{
       "Global MG94xREV":0.003473875423912177,
       "Nucleotide GTR":0.003374436490976879,
       "original name":"gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human"
      },
     "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":{
       "Global MG94xREV":0.003465962442102671,
       "Nucleotide GTR":0.003376034743011948,
       "original name":"gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human"
      },
     "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":{
       "Global MG94xREV":0.003468563557182978,
       "Nucleotide GTR":0.003374190741831846,
       "original name":"gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human"
      },
     "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":{
       "Global MG94xREV":0.003465082984487299,
       "Nucleotide GTR":0.003376937492543959,
       "original name":"gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human"
      }
    },
   "attributes":{
     "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] 
      ],
     "name":"fel.filter.default"
    }
  },
 "fits":{
   "Global MG94xREV":{
     "AIC-c":2512.992528252278,
     "Equilibrium frequencies":      [
[0.03825952761243274],
      [0.01370948533169502],
      [0.0238326285579188],
      [0.05169206288834598],
      [0.02910782227384961],
      [0.01043016700423795],
      [0.01813184740308045],
      [0.03932728586627101],
      [0.01035067712195123],
      [0.003708944282165923],
      [0.006447644771501305],
      [0.01398469573761802],
      [0.0283653688047424],
      [0.01016412464618009],
      [0.01766935821790241],
      [0.03832416445281453],
      [0.01521889661505549],
      [0.005453366858635389],
      [0.009480156518454269],
      [0.02056209812326697],
      [0.01157852606970437],
      [0.004148917752546374],
      [0.007212496554133422],
      [0.01564363009947405],
      [0.00411729822204095],
      [0.001475345962268018],
      [0.002564747797779777],
      [0.005562840210150803],
      [0.01128319250724396],
      [0.004043091272315801],
      [0.007028527343480687],
      [0.01524460789411934],
      [0.03592403244011121],
      [0.01287261047188149],
      [0.02237780168434643],
      [0.04853659885475865],
      [0.02733097915424774],
      [0.009793473186905268],
      [0.01702501611901085],
      [0.03692661100139533],
      [0.009718835644621534],
      [0.003482537371104292],
      [0.0060540580187001],
      [0.01313102107355921],
      [0.02663384763763138],
      [0.009543670983435077],
      [0.01659075888876379],
      [0.0359847236220365],
      [0.00848480075962617],
      [0.03199221880690793],
      [0.01801483181642438],
      [0.006455230577911434],
      [0.01122180073845716],
      [0.02433965804833868],
      [0.002295465694104339],
      [0.003990447484454917],
      [0.008655128485630147],
      [0.01755532734880559],
      [0.00629057695692368],
      [0.01093556617204019],
      [0.02371882618448924] 
      ],
     "Log Likelihood":-1204.057620166247,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *B-1-617*":        [
[21.18256593595067, 1] 
        ],
       "non-synonymous/synonymous rate ratio for *Reference*":        [
[0, 1] 
        ],
       "non-synonymous/synonymous rate ratio for *background*":        [
[0.5156677174296214, 1] 
        ]
      },
     "display order":1,
     "estimated parameters":52
    },
   "Nucleotide GTR":{
     "AIC-c":2633.0046471406,
     "Equilibrium frequencies":      [
[0.3251262626262627],
      [0.1799242424242424],
      [0.2026515151515151],
      [0.2922979797979798] 
      ],
     "Log Likelihood":-1247.247280799152,
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0.3101631549852981,
       "Substitution rate from nucleotide C to nucleotide G":1.129990583516242,
       "Substitution rate from nucleotide C to nucleotide T":2.723444388603395,
       "Substitution rate from nucleotide G to nucleotide T":1.720896006888861
      },
     "display order":0,
     "estimated parameters":69
    }
  },
 "input":{
   "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas",
   "number of sequences":32,
   "number of sites":198,
   "partition count":1,
   "trees":{
     "0":"(REFERENCE,(gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human,epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021)Node20,gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human,epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021,(epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021,gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human)Node4,epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021,gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human,gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human,epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021,gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human,(gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human,gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human,epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021)Node38,epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021,gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human,epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021,gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human,epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021,epi_isl_1543980_hCoV_19_Singapore_490_2021,epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021,gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human,epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021,gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human,gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human,epi_isl_1652118_hCoV_19_Singapore_575_2021,epi_isl_1652105_hCoV_19_Singapore_561_2021,gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human,gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human,epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)"
    }
  },
 "tested":{
   "0":{
     "Node20":"B-1-617",
     "Node38":"Reference",
     "Node4":"B-1-617",
     "REFERENCE":"background",
     "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"background",
     "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"background",
     "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"background",
     "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"background",
     "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"background",
     "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"background",
     "epi_isl_1543980_hCoV_19_Singapore_490_2021":"background",
     "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"background",
     "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"background",
     "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"background",
     "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"background",
     "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"background",
     "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"background",
     "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"background",
     "epi_isl_1652105_hCoV_19_Singapore_561_2021":"background",
     "epi_isl_1652118_hCoV_19_Singapore_575_2021":"background",
     "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"background",
     "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"background",
     "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"background",
     "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"background",
     "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"background",
     "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"background",
     "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"background",
     "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":"background",
     "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":"background",
     "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"background",
     "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"background",
     "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"background",
     "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"background",
     "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"background",
     "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"background"
    }
  },
 "timers":{
   "FEL analysis":{
     "order":2,
     "timer":9
    },
   "Model fitting":{
     "order":1,
     "timer":5
    },
   "Total time":{
     "order":0,
     "timer":14
    }
  }
}