diff test-data/relax-out1.json @ 2:a88848771d2d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author iuc
date Tue, 27 Apr 2021 18:01:42 +0000
parents df56795c3d89
children e6009f23582c
line wrap: on
line diff
--- a/test-data/relax-out1.json	Tue Apr 20 19:53:07 2021 +0000
+++ b/test-data/relax-out1.json	Tue Apr 27 18:01:42 2021 +0000
@@ -1,486 +1,174 @@
 {
- "analysis":{
-   "info":"RELAX (a random effects test of selection relaxation) uses a random effects branch-site model framework to test whether a set of 'Test' branches evolves under relaxed selection relative to a set of 'Reference' branches (R), as measured by the relaxation parameter (K).\n                                                Version 2.1 adds a check for stability in K estimates to try to mitigate convergence problems",
-   "version":"2.1",
-   "citation":"RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015). Mol Biol Evol 32 (3): 820-832",
-   "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
-   "contact":"spond@temple.edu",
-   "requirements":"in-frame codon alignment and a phylogenetic tree, with at least two groups of branches defined using the {} notation (one group can be defined as all unlabeled branches)"
-  },
- "input":{
-   "file name":"/home/galaxystaging/galaxy/database/jobs_directory/000/79/working/relax_input.fa",
-   "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":-3531.964032193222,
-     "estimated parameters":24,
-     "AIC-c":7112.142925621896,
-     "Equilibrium frequencies":[
-      [0.3563279857397504],
-      [0.1837789661319073],
-      [0.2402852049910873],
-      [0.2196078431372549]
-      ],
-     "Rate Distributions":{
-       "Substitution rate from nucleotide A to nucleotide C":0.5465757107930838,
-       "Substitution rate from nucleotide A to nucleotide G":1,
-       "Substitution rate from nucleotide A to nucleotide T":0.264131123736109,
-       "Substitution rate from nucleotide C to nucleotide G":0.4861812992450388,
-       "Substitution rate from nucleotide C to nucleotide T":1.017887589835735,
-       "Substitution rate from nucleotide G to nucleotide T":0.3021773696987065
-      },
-     "display order":0
-    },
-   "MG94xREV with separate rates for branch sets":{
-     "Log Likelihood":-3460.931903299487,
-     "estimated parameters":32,
-     "AIC-c":6987.013507197776,
-     "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],
-      [0.01020486315060615],
-      [0.01263311863778268],
-      [0.01061792547971484],
-      [0.01306446616325414],
-      [0.01067875601941112],
-      [0.01321977470017749],
-      [0.01111100011404158],
-      [0.01921770557551369],
-      [0.01570834862514353],
-      [0.01944616295744266],
-      [0.01634417558076203],
-      [0.01975257768318274],
-      [0.02055210293142003],
-      [0.009176034326710849],
-      [0.007500393094996483],
-      [0.00928511773266342],
-      [0.007803986567571961],
-      [0.00784869593340758],
-      [0.009716299514778986],
-      [0.008166387662818644],
-      [0.01412467213650941],
-      [0.01154535713247913],
-      [0.01429258425298098],
-      [0.01201267864744234]
-      ],
-     "Rate Distributions":{
-       "non-synonymous/synonymous rate ratio for *Reference*":[
-        [1.617765969026557, 1]
-        ],
-       "non-synonymous/synonymous rate ratio for *Test*":[
-        [0.7687683974183303, 1]
-        ]
-      },
-     "display order":1
-    },
-   "General descriptive":{
-     "Log Likelihood":-3420.975369746331,
-     "estimated parameters":51,
-     "AIC-c":6946.868231241836,
-     "Rate Distributions":{
-       "Shared":{
-         "0":{
-           "omega":1e-08,
-           "proportion":0.2345034364701236
-          },
-         "1":{
-           "omega":1e-08,
-           "proportion":0.3180344596999608
-          },
-         "2":{
-           "omega":6.64943557055033,
-           "proportion":0.4474621038299156
-          }
-        }
-      },
-     "display order":4
-    },
-   "RELAX alternative":{
-     "Log Likelihood":-3429.125323833579,
-     "estimated parameters":36,
-     "AIC-c":6931.704002822642,
-     "Rate Distributions":{
-       "Test":{
-         "0":{
-           "omega":0,
-           "proportion":0.1993913071931658
-          },
-         "1":{
-           "omega":0,
-           "proportion":0.3360341729181165
-          },
-         "2":{
-           "omega":2.153056268947235,
-           "proportion":0.4645745198887177
-          }
-        },
-       "Reference":{
-         "0":{
-           "omega":0,
-           "proportion":0.1993913071931658
-          },
-         "1":{
-           "omega":0,
-           "proportion":0.3360341729181165
-          },
-         "2":{
-           "omega":6.166712663934246,
-           "proportion":0.4645745198887177
-          }
-        }
-      },
-     "display order":2
-    },
-   "RELAX null":{
-     "Log Likelihood":-3437.187429488768,
-     "estimated parameters":35,
-     "AIC-c":6945.748904779063,
-     "Rate Distributions":{
-       "Test":{
-         "0":{
-           "omega":0.1177689533662908,
-           "proportion":0.4926494715348529
-          },
-         "1":{
-           "omega":0.3195682613972807,
-           "proportion":0.1517366025099117
-          },
-         "2":{
-           "omega":3.893733071412322,
-           "proportion":0.3556139259552353
-          }
-        },
-       "Reference":{
-         "0":{
-           "omega":0.1177689533662908,
-           "proportion":0.4926494715348529
-          },
-         "1":{
-           "omega":0.3195682613972807,
-           "proportion":0.1517366025099117
-          },
-         "2":{
-           "omega":3.893733071412322,
-           "proportion":0.3556139259552353
-          }
-        }
-      },
-     "display order":3
-    },
-   "RELAX partitioned descriptive":{
-     "Log Likelihood":-3427.515821600644,
-     "estimated parameters":40,
-     "AIC-c":6936.824972889643,
-     "Rate Distributions":{
-       "Test":{
-         "0":{
-           "omega":0.2264899618249929,
-           "proportion":0.1370778077745601
-          },
-         "1":{
-           "omega":0.2328054750512875,
-           "proportion":0.6322930022247097
-          },
-         "2":{
-           "omega":4.13407071706127,
-           "proportion":0.2306291900007301
-          }
-        },
-       "Reference":{
-         "0":{
-           "omega":0,
-           "proportion":0.09054841512283768
-          },
-         "1":{
-           "omega":0,
-           "proportion":0.4231976237742962
-          },
-         "2":{
-           "omega":5.975493863572218,
-           "proportion":0.4862539611028661
-          }
-        }
-      },
-     "display order":5
-    }
-  },
- "timers":{
-   "Overall":{
-     "timer":562,
-     "order":0
-    },
-   "Preliminary model fitting":{
-     "timer":33,
-     "order":1
-    },
-   "General descriptive model fitting":{
-     "timer":256,
-     "order":2
-    },
-   "RELAX alternative model fitting":{
-     "timer":78,
-     "order":3
-    },
-   "RELAX null model fitting":{
-     "timer":98,
-     "order":4
-    },
-   "RELAX partitioned descriptive":{
-     "timer":95,
-     "order":5
-    }
-  },
- "test results":{
-   "LRT":16.12421131037809,
-   "p-value":5.932080525117289e-05,
-   "relaxation or intensification parameter":0.4215604262166031
-  },
- "tested":{
-   "0":{
-     "Pig":"Test",
-     "Cow":"Reference",
-     "Node3":"Test",
-     "Horse":"Reference",
-     "Cat":"Reference",
-     "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":"relax.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]
-      ]
-    }
-  },
+ "analysis":0,
  "branch attributes":{
    "0":{
-     "Human":{
-       "original name":"Human",
-       "Nucleotide GTR":0,
-       "MG94xREV with separate rates for branch sets":0,
-       "General descriptive":0,
-       "k (general descriptive)":0.7168352052656061,
-       "RELAX alternative":0,
-       "RELAX null":0,
-       "RELAX partitioned descriptive":0
-      },
-     "Chimp":{
-       "original name":"Chimp",
-       "Nucleotide GTR":0.001818722292071369,
-       "MG94xREV with separate rates for branch sets":0.001828056639868651,
-       "General descriptive":0.001850581335499795,
-       "k (general descriptive)":2.329184252362038,
-       "RELAX alternative":0.001831548027528597,
-       "RELAX null":0.001835680183060623,
-       "RELAX partitioned descriptive":0.00183255534978807
-      },
      "Baboon":{
-       "original name":"Baboon",
-       "Nucleotide GTR":0.001682319705247233,
-       "MG94xREV with separate rates for branch sets":0.001770013551346919,
-       "General descriptive":0.001869883333754939,
-       "k (general descriptive)":0.1228116964827354,
-       "RELAX alternative":0.001867314836287998,
-       "RELAX null":0.001853697678697539,
-       "RELAX partitioned descriptive":0.00189422569191071
-      },
-     "RhMonkey":{
-       "original name":"RhMonkey",
-       "Nucleotide GTR":0.003776495523121213,
-       "MG94xREV with separate rates for branch sets":0.003720554271464007,
-       "General descriptive":0.003663070393385353,
-       "k (general descriptive)":2.272939790126477,
-       "RELAX alternative":0.003641537789305734,
-       "RELAX null":0.003670955010908306,
-       "RELAX partitioned descriptive":0.003632158699516803
-      },
-     "Cow":{
-       "original name":"Cow",
-       "Nucleotide GTR":0.2483201583381086,
-       "MG94xREV with separate rates for branch sets":0.2522875145085426,
-       "General descriptive":0.3735091756053704,
-       "k (general descriptive)":1.19957642031092,
-       "RELAX alternative":0.3407703477665083,
-       "RELAX null":0.2958310860090909,
-       "RELAX partitioned descriptive":0.3460604457589064
-      },
-     "Pig":{
-       "original name":"Pig",
-       "Nucleotide GTR":0.1871417867164377,
-       "MG94xREV with separate rates for branch sets":0.1903173961963296,
-       "General descriptive":0.2109384940367451,
-       "k (general descriptive)":0.6656155688777629,
-       "RELAX alternative":0.197167672065417,
-       "RELAX null":0.2182629931612711,
-       "RELAX partitioned descriptive":0.2076369268997903
-      },
-     "Horse":{
-       "original name":"Horse",
-       "Nucleotide GTR":0.2091567334932583,
-       "MG94xREV with separate rates for branch sets":0.2159358728261337,
-       "General descriptive":0.2810540078141565,
-       "k (general descriptive)":0.8115699858212525,
-       "RELAX alternative":0.3032889682089364,
-       "RELAX null":0.2571098559672552,
-       "RELAX partitioned descriptive":0.3026705354406338
+       "General descriptive":0.001858767762813579,
+       "MG94xREV with separate rates for branch sets":0.001769472024099301,
+       "Nucleotide GTR":0.001680040630127455,
+       "RELAX alternative":0.001872256662230973,
+       "RELAX null":0.001855569334462731,
+       "RELAX partitioned descriptive":0.001898170574782418,
+       "k (general descriptive)":0.09971581394819819,
+       "original name":"Baboon"
       },
      "Cat":{
-       "original name":"Cat",
-       "Nucleotide GTR":0.2660040109418023,
-       "MG94xREV with separate rates for branch sets":0.2795692100037539,
-       "General descriptive":0.3635335087937213,
-       "k (general descriptive)":0.9728289997736356,
-       "RELAX alternative":0.3660889485578829,
-       "RELAX null":0.3281803512051322,
-       "RELAX partitioned descriptive":0.370631318143086
+       "General descriptive":0.3644803308678196,
+       "MG94xREV with separate rates for branch sets":0.2796030091674721,
+       "Nucleotide GTR":0.2660909938917123,
+       "RELAX alternative":0.3689219388980864,
+       "RELAX null":0.3256077554105627,
+       "RELAX partitioned descriptive":0.3717219559832593,
+       "k (general descriptive)":2.314507643873676,
+       "original name":"Cat"
+      },
+     "Chimp":{
+       "General descriptive":0.001848680051431209,
+       "MG94xREV with separate rates for branch sets":0.001825434296531533,
+       "Nucleotide GTR":0.001818373670119325,
+       "RELAX alternative":0.001831703934281931,
+       "RELAX null":0.00183525802483954,
+       "RELAX partitioned descriptive":0.001832717232153088,
+       "k (general descriptive)":5.261186652622472,
+       "original name":"Chimp"
+      },
+     "Cow":{
+       "General descriptive":0.3733627618450006,
+       "MG94xREV with separate rates for branch sets":0.2520490246808783,
+       "Nucleotide GTR":0.2481025999892287,
+       "RELAX alternative":0.342739998512865,
+       "RELAX null":0.2948256709356563,
+       "RELAX partitioned descriptive":0.3466331923230422,
+       "k (general descriptive)":2.846155982935764,
+       "original name":"Cow"
+      },
+     "Horse":{
+       "General descriptive":0.2802176313870697,
+       "MG94xREV with separate rates for branch sets":0.2158304510870495,
+       "Nucleotide GTR":0.2090310577070883,
+       "RELAX alternative":0.3058487498567987,
+       "RELAX null":0.2559911331878715,
+       "RELAX partitioned descriptive":0.3034694616209482,
+       "k (general descriptive)":1.926646959057857,
+       "original name":"Horse"
+      },
+     "Human":{
+       "General descriptive":0,
+       "MG94xREV with separate rates for branch sets":0,
+       "Nucleotide GTR":0,
+       "RELAX alternative":0,
+       "RELAX null":0,
+       "RELAX partitioned descriptive":0,
+       "k (general descriptive)":1.462532487172471,
+       "original name":"Human"
       },
      "Mouse":{
-       "original name":"Mouse",
-       "Nucleotide GTR":0.1182531454610134,
-       "MG94xREV with separate rates for branch sets":0.1199409901922202,
-       "General descriptive":0.1313354563273305,
-       "k (general descriptive)":0.2294495132372282,
-       "RELAX alternative":0.1341640738853253,
-       "RELAX null":0.1483938193994467,
-       "RELAX partitioned descriptive":0.1476318125310598
-      },
-     "Rat":{
-       "original name":"Rat",
-       "Nucleotide GTR":0.06669544716210057,
-       "MG94xREV with separate rates for branch sets":0.06725647453745125,
-       "General descriptive":0.07175915155128718,
-       "k (general descriptive)":0.5208088414555363,
-       "RELAX alternative":0.0724007498013708,
-       "RELAX null":0.07365614414375878,
-       "RELAX partitioned descriptive":0.07568744563050285
+       "General descriptive":0.1307950021191255,
+       "MG94xREV with separate rates for branch sets":0.1197727080219867,
+       "Nucleotide GTR":0.1180171198334285,
+       "RELAX alternative":0.1346501492117481,
+       "RELAX null":0.1468861666244963,
+       "RELAX partitioned descriptive":0.1475623398849678,
+       "k (general descriptive)":0.4639609139295889,
+       "original name":"Mouse"
       },
      "Node1":{
-       "Nucleotide GTR":0.2771601504028877,
-       "MG94xREV with separate rates for branch sets":0.286127507474972,
-       "General descriptive":0.3532216661512288,
-       "k (general descriptive)":0.2199586786715634,
-       "RELAX alternative":0.3833004811985787,
-       "RELAX null":0.4576044234710181,
-       "RELAX partitioned descriptive":0.4360897576025625
+       "General descriptive":0.350050900813081,
+       "MG94xREV with separate rates for branch sets":0.2857356440257563,
+       "Nucleotide GTR":0.2767237570684924,
+       "RELAX alternative":0.3856490868629754,
+       "RELAX null":0.4521046025119397,
+       "RELAX partitioned descriptive":0.4358952685746469,
+       "k (general descriptive)":0.458870761901378
       },
      "Node12":{
-       "Nucleotide GTR":0.01783222754921504,
-       "MG94xREV with separate rates for branch sets":0.01799298835381691,
-       "General descriptive":0.01771170858901891,
-       "k (general descriptive)":0.1560499010177516,
-       "RELAX alternative":0.01833338832069913,
-       "RELAX null":0.01828012634520382,
-       "RELAX partitioned descriptive":0.01877701767421286
+       "General descriptive":0.01766384491594095,
+       "MG94xREV with separate rates for branch sets":0.01800001211221997,
+       "Nucleotide GTR":0.01784803874223016,
+       "RELAX alternative":0.01835132674304535,
+       "RELAX null":0.0182458522959868,
+       "RELAX partitioned descriptive":0.01878351896299688,
+       "k (general descriptive)":0.1241597340554799
       },
      "Node2":{
-       "Nucleotide GTR":0.06619118337434968,
-       "MG94xREV with separate rates for branch sets":0.06192085035608558,
-       "General descriptive":0.05843310574046084,
-       "k (general descriptive)":0.2816499194095207,
-       "RELAX alternative":0.05469841675490748,
-       "RELAX null":0.06219694236954142,
-       "RELAX partitioned descriptive":0.06011281230238084
+       "General descriptive":0.05771641706257456,
+       "MG94xREV with separate rates for branch sets":0.06169547093990335,
+       "Nucleotide GTR":0.06613162123865737,
+       "RELAX alternative":0.05450381496370671,
+       "RELAX null":0.06144358908741494,
+       "RELAX partitioned descriptive":0.05974179966710006,
+       "k (general descriptive)":0.5400661932123572
       },
      "Node3":{
-       "Nucleotide GTR":0.09883746945145887,
-       "MG94xREV with separate rates for branch sets":0.09744342239018626,
-       "General descriptive":0.1340338084149808,
-       "k (general descriptive)":0.8358980179450297,
-       "RELAX alternative":0.1164056814082033,
-       "RELAX null":0.1282588343299434,
-       "RELAX partitioned descriptive":0.1194563668460339
+       "General descriptive":0.133048972566238,
+       "MG94xREV with separate rates for branch sets":0.09736816312927643,
+       "Nucleotide GTR":0.09886326330774685,
+       "RELAX alternative":0.1168284793254293,
+       "RELAX null":0.1276889506286756,
+       "RELAX partitioned descriptive":0.1195376339442456,
+       "k (general descriptive)":1.980345386854111
       },
      "Node8":{
-       "Nucleotide GTR":0.106110061225871,
-       "MG94xREV with separate rates for branch sets":0.1090208137603471,
-       "General descriptive":0.1401594332730181,
-       "k (general descriptive)":0.9135621448569878,
-       "RELAX alternative":0.1275155316795084,
-       "RELAX null":0.1346842719904758,
-       "RELAX partitioned descriptive":0.1358683972849559
+       "General descriptive":0.1404364853762839,
+       "MG94xREV with separate rates for branch sets":0.1092041281639667,
+       "Nucleotide GTR":0.106239268140425,
+       "RELAX alternative":0.1283918913740865,
+       "RELAX null":0.1343238120118072,
+       "RELAX partitioned descriptive":0.1363833239244288,
+       "k (general descriptive)":2.210166852936262
       },
      "Node9":{
-       "Nucleotide GTR":0.02567391471029082,
-       "MG94xREV with separate rates for branch sets":0.02582385148170195,
-       "General descriptive":0.02665352479510937,
-       "k (general descriptive)":0.1089752436854629,
-       "RELAX alternative":0.02681134359856903,
-       "RELAX null":0.02759760291393045,
-       "RELAX partitioned descriptive":0.02746061131173372
+       "General descriptive":0.02665050120918479,
+       "MG94xREV with separate rates for branch sets":0.02578196090462333,
+       "Nucleotide GTR":0.02566573875750134,
+       "RELAX alternative":0.02679622227446188,
+       "RELAX null":0.02754241929890747,
+       "RELAX partitioned descriptive":0.0274479920792393,
+       "k (general descriptive)":0.0733131770696667
+      },
+     "Pig":{
+       "General descriptive":0.2104601216238473,
+       "MG94xREV with separate rates for branch sets":0.1902977811335351,
+       "Nucleotide GTR":0.1871893456388788,
+       "RELAX alternative":0.19752905148822,
+       "RELAX null":0.2165309177979844,
+       "RELAX partitioned descriptive":0.2074828949843082,
+       "k (general descriptive)":1.577441472516679,
+       "original name":"Pig"
+      },
+     "Rat":{
+       "General descriptive":0.07164210204456434,
+       "MG94xREV with separate rates for branch sets":0.06709541225974219,
+       "Nucleotide GTR":0.06661283005976348,
+       "RELAX alternative":0.07247047023746757,
+       "RELAX null":0.07343093575256582,
+       "RELAX partitioned descriptive":0.07560655472076994,
+       "k (general descriptive)":1.318174884032695,
+       "original name":"Rat"
+      },
+     "RhMonkey":{
+       "General descriptive":0.003674505194636419,
+       "MG94xREV with separate rates for branch sets":0.003716165486244973,
+       "Nucleotide GTR":0.003775170135617877,
+       "RELAX alternative":0.003636176595806718,
+       "RELAX null":0.003665938723426083,
+       "RELAX partitioned descriptive":0.003624376345656283,
+       "k (general descriptive)":5.171610533872274,
+       "original name":"RhMonkey"
       }
     },
    "attributes":{
-     "original name":{
-       "attribute type":"node label",
-       "display order":-1
-      },
-     "Nucleotide GTR":{
+     "General descriptive":{
        "attribute type":"branch length",
-       "display order":0
+       "display order":4
       },
      "MG94xREV with separate rates for branch sets":{
        "attribute type":"branch length",
        "display order":1
       },
-     "General descriptive":{
+     "Nucleotide GTR":{
        "attribute type":"branch length",
-       "display order":4
-      },
-     "k (general descriptive)":{
-       "attribute type":"branch label",
-       "display order":4
+       "display order":0
       },
      "RELAX alternative":{
        "attribute type":"branch length",
@@ -493,7 +181,312 @@
      "RELAX partitioned descriptive":{
        "attribute type":"branch length",
        "display order":5
+      },
+     "k (general descriptive)":{
+       "attribute type":"branch label",
+       "display order":4
+      },
+     "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] 
+      ],
+     "name":"relax.filter.default"
+    }
+  },
+ "fits":{
+   "General descriptive":{
+     "AIC-c":6945.891353881681,
+     "Log Likelihood":-3420.486931066253,
+     "Rate Distributions":{
+       "Shared":{
+         "0":{
+           "omega":2.202835393423959e-18,
+           "proportion":0.4487473029633234
+          },
+         "1":{
+           "omega":2.202835393423959e-18,
+           "proportion":0.09729227592412616
+          },
+         "2":{
+           "omega":2.202835210940273,
+           "proportion":0.4539604211125504
+          }
+        }
+      },
+     "display order":4,
+     "estimated parameters":51
+    },
+   "MG94xREV with separate rates for branch sets":{
+     "AIC-c":6987.565999172035,
+     "Equilibrium frequencies":      [
+[0.04876086397632926],
+      [0.03982224127745371],
+      [0.0494959405650269],
+      [0.04152830682371345],
+      [0.01810345074594235],
+      [0.01478480742075003],
+      [0.01837636270304883],
+      [0.01541821854326533],
+      [0.01892910005547028],
+      [0.01545910240515689],
+      [0.01921445878706794],
+      [0.01612140169177368],
+      [0.02829747763884322],
+      [0.02311011106415996],
+      [0.02872406592369408],
+      [0.02410019507229243],
+      [0.01663805943190806],
+      [0.01358804506433061],
+      [0.01688888041768248],
+      [0.01417018446135155],
+      [0.006177213955434187],
+      [0.005044834822351987],
+      [0.006270336287397383],
+      [0.00526096577332031],
+      [0.006458939937330408],
+      [0.005274916061901906],
+      [0.006556309326397028],
+      [0.005500904159606446],
+      [0.009655594186286731],
+      [0.007885574003572761],
+      [0.009801153568494354],
+      [0.008223407979974132],
+      [0.03327785448210915],
+      [0.02717750758119989],
+      [0.03377952261833742],
+      [0.02834184710178207],
+      [0.01235507229404208],
+      [0.01009019590244688],
+      [0.01254132667213156],
+      [0.01052248035033209],
+      [0.01291855364640413],
+      [0.01055038238273567],
+      [0.01311330258173711],
+      [0.01100238215235291],
+      [0.01931219560697892],
+      [0.0157719705998612],
+      [0.01960332955558842],
+      [0.01644767379420349],
+      [0.01965132601881859],
+      [0.02049322866376102],
+      [0.008933621043463411],
+      [0.007295949736387736],
+      [0.009068296583349953],
+      [0.007608523013862737],
+      [0.007628698224327205],
+      [0.009481877006094248],
+      [0.00795552712159237],
+      [0.01396413011303752],
+      [0.01140428846505027],
+      [0.01417464125436193],
+      [0.01189287130232129] 
+      ],
+     "Log Likelihood":-3461.208149286616,
+     "Rate Distributions":{
+       "non-synonymous/synonymous rate ratio for *Reference*":        [
+[0.7682335289209781, 1] 
+        ],
+       "non-synonymous/synonymous rate ratio for *Test*":        [
+[1.605439824256426, 1] 
+        ]
+      },
+     "display order":1,
+     "estimated parameters":32
+    },
+   "Nucleotide GTR":{
+     "AIC-c":7112.857310169033,
+     "Equilibrium frequencies":      [
+[0.3592490842490842],
+      [0.181959706959707],
+      [0.240018315018315],
+      [0.2187728937728937] 
+      ],
+     "Log Likelihood":-3532.32122446679,
+     "Rate Distributions":{
+       "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,
+       "Substitution rate from nucleotide A to nucleotide G":1,
+       "Substitution rate from nucleotide A to nucleotide T":0.2647746107611847,
+       "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032,
+       "Substitution rate from nucleotide C to nucleotide T":1.02837595903795,
+       "Substitution rate from nucleotide G to nucleotide T":0.304509117524575
+      },
+     "display order":0,
+     "estimated parameters":24
+    },
+   "RELAX alternative":{
+     "AIC-c":6931.922980697387,
+     "Log Likelihood":-3429.234812770952,
+     "Rate Distributions":{
+       "Reference":{
+         "0":{
+           "omega":1.762268314739328e-19,
+           "proportion":0.4504132080156107
+          },
+         "1":{
+           "omega":1.762268314739328e-19,
+           "proportion":0.08749553114962015
+          },
+         "2":{
+           "omega":2.19971015101232,
+           "proportion":0.4620912608347691
+          }
+        },
+       "Test":{
+         "0":{
+           "omega":1.054840660215593e-44,
+           "proportion":0.4504132080156107
+          },
+         "1":{
+           "omega":1.054840660215593e-44,
+           "proportion":0.08749553114962015
+          },
+         "2":{
+           "omega":6.350765030542244,
+           "proportion":0.4620912608347691
+          }
+        }
+      },
+     "display order":2,
+     "estimated parameters":36
+    },
+   "RELAX null":{
+     "AIC-c":6946.046672507471,
+     "Log Likelihood":-3437.336313352972,
+     "Rate Distributions":{
+       "Reference":{
+         "0":{
+           "omega":0.1150006822953211,
+           "proportion":0.542405144031307
+          },
+         "1":{
+           "omega":0.2401508033814633,
+           "proportion":0.08223353569636478
+          },
+         "2":{
+           "omega":3.69263720947284,
+           "proportion":0.3753613202723282
+          }
+        },
+       "Test":{
+         "0":{
+           "omega":0.1150006822953211,
+           "proportion":0.542405144031307
+          },
+         "1":{
+           "omega":0.2401508033814633,
+           "proportion":0.08223353569636478
+          },
+         "2":{
+           "omega":3.69263720947284,
+           "proportion":0.3753613202723282
+          }
+        }
+      },
+     "display order":3,
+     "estimated parameters":35
+    },
+   "RELAX partitioned descriptive":{
+     "AIC-c":6937.04707353565,
+     "Log Likelihood":-3427.626871923648,
+     "Rate Distributions":{
+       "Reference":{
+         "0":{
+           "omega":0.1943306885168281,
+           "proportion":0.3359458135547653
+          },
+         "1":{
+           "omega":0.2607558478587815,
+           "proportion":0.4332550437039296
+          },
+         "2":{
+           "omega":4.134271224300374,
+           "proportion":0.2307991427413052
+          }
+        },
+       "Test":{
+         "0":{
+           "omega":0,
+           "proportion":0.4753488415962343
+          },
+         "1":{
+           "omega":0,
+           "proportion":0.03858318603767072
+          },
+         "2":{
+           "omega":6.017221959238516,
+           "proportion":0.486067972366095
+          }
+        }
+      },
+     "display order":5,
+     "estimated parameters":40
+    }
+  },
+ "input":{
+   "file name":"/tmp/tmpbauyxvdv/job_working_directory/000/3/working/./input.fasta",
+   "number of sequences":10,
+   "number of sites":187,
+   "partition count":1,
+   "trees":{
+     "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,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)"
+    }
+  },
+ "test results":{
+   "LRT":16.20300116404087,
+   "p-value":5.690389451429301e-05,
+   "relaxation or intensification parameter":2.344938789085876
+  },
+ "tested":{
+   "0":{
+     "Baboon":"Reference",
+     "Cat":"Test",
+     "Chimp":"Reference",
+     "Cow":"Test",
+     "Horse":"Test",
+     "Human":"Reference",
+     "Mouse":"Reference",
+     "Node1":"Reference",
+     "Node12":"Reference",
+     "Node2":"Reference",
+     "Node3":"Reference",
+     "Node8":"Reference",
+     "Node9":"Reference",
+     "Pig":"Reference",
+     "Rat":"Reference",
+     "RhMonkey":"Reference"
+    }
+  },
+ "timers":{
+   "General descriptive model fitting":{
+     "order":2,
+     "timer":132
+    },
+   "Overall":{
+     "order":0,
+     "timer":324
+    },
+   "Preliminary model fitting":{
+     "order":1,
+     "timer":8
+    },
+   "RELAX alternative model fitting":{
+     "order":3,
+     "timer":65
+    },
+   "RELAX null model fitting":{
+     "order":4,
+     "timer":66
+    },
+   "RELAX partitioned descriptive":{
+     "order":5,
+     "timer":53
+    }
   }
 }
\ No newline at end of file