--- a/test-data/relax-out1.json	Thu Mar 02 15:02:12 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,493 +0,0 @@
-{
- "analysis":0,
- "branch attributes":{
-   "0":{
-     "Baboon":{
-       "General descriptive":0.001859058366368826,
-       "MG94xREV with separate rates for branch sets":0.001769294089885709,
-       "Nucleotide GTR":0.001685167654714891,
-       "RELAX alternative":0.001873708670384941,
-       "RELAX null":0.001859167714920677,
-       "RELAX partitioned descriptive":0.001898817195216417,
-       "k (general descriptive)":0.09969742933359635,
-       "original name":"Baboon"
-      },
-     "Cat":{
-       "General descriptive":0.3650161006190072,
-       "MG94xREV with separate rates for branch sets":0.2796018473093496,
-       "Nucleotide GTR":0.2660536011315811,
-       "RELAX alternative":0.3685874431614762,
-       "RELAX null":0.3167334440346762,
-       "RELAX partitioned descriptive":0.3719472357609613,
-       "k (general descriptive)":2.319877215422834,
-       "original name":"Cat"
-      },
-     "Chimp":{
-       "General descriptive":0.001895983937468787,
-       "MG94xREV with separate rates for branch sets":0.001826027667597702,
-       "Nucleotide GTR":0.001820258053351119,
-       "RELAX alternative":0.001831530791728368,
-       "RELAX null":0.001834052740714585,
-       "RELAX partitioned descriptive":0.001832682515795942,
-       "k (general descriptive)":5.158328270628251,
-       "original name":"Chimp"
-      },
-     "Cow":{
-       "General descriptive":0.3737128696500712,
-       "MG94xREV with separate rates for branch sets":0.2521304147607955,
-       "Nucleotide GTR":0.2480198736772598,
-       "RELAX alternative":0.3426997068768813,
-       "RELAX null":0.2931467439343907,
-       "RELAX partitioned descriptive":0.3469082289876269,
-       "k (general descriptive)":2.852150041266453,
-       "original name":"Cow"
-      },
-     "Horse":{
-       "General descriptive":0.2804279827409984,
-       "MG94xREV with separate rates for branch sets":0.2158535884657318,
-       "Nucleotide GTR":0.2090998951755368,
-       "RELAX alternative":0.3058441352816696,
-       "RELAX null":0.2546949756245578,
-       "RELAX partitioned descriptive":0.3035514182923183,
-       "k (general descriptive)":1.929916608813313,
-       "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)":1.485684693044203,
-       "original name":"Human"
-      },
-     "Mouse":{
-       "General descriptive":0.1308809509233143,
-       "MG94xREV with separate rates for branch sets":0.1197584101055861,
-       "Nucleotide GTR":0.1181058300538561,
-       "RELAX alternative":0.1346294129227689,
-       "RELAX null":0.1438267359449897,
-       "RELAX partitioned descriptive":0.148454172127534,
-       "k (general descriptive)":0.4625550584398252,
-       "original name":"Mouse"
-      },
-     "Node1":{
-       "General descriptive":0.3500691487967139,
-       "MG94xREV with separate rates for branch sets":0.2856782993656827,
-       "Nucleotide GTR":0.2767105173979571,
-       "RELAX alternative":0.385503346940632,
-       "RELAX null":0.4352096867868785,
-       "RELAX partitioned descriptive":0.4379872513902164,
-       "k (general descriptive)":0.4572754180074107
-      },
-     "Node12":{
-       "General descriptive":0.01767932040676307,
-       "MG94xREV with separate rates for branch sets":0.01800350744117403,
-       "Nucleotide GTR":0.01784222107494562,
-       "RELAX alternative":0.01834159481548459,
-       "RELAX null":0.01822563245625142,
-       "RELAX partitioned descriptive":0.01881534539472323,
-       "k (general descriptive)":0.1240073621579099
-      },
-     "Node2":{
-       "General descriptive":0.05767151047612454,
-       "MG94xREV with separate rates for branch sets":0.06170856993599769,
-       "Nucleotide GTR":0.06614755778044307,
-       "RELAX alternative":0.0544792799094392,
-       "RELAX null":0.06013052353393462,
-       "RELAX partitioned descriptive":0.0601550105387935,
-       "k (general descriptive)":0.5400834620465133
-      },
-     "Node3":{
-       "General descriptive":0.1330088052861041,
-       "MG94xREV with separate rates for branch sets":0.09733132151710643,
-       "Nucleotide GTR":0.09883748387954429,
-       "RELAX alternative":0.1169235247351394,
-       "RELAX null":0.1263887172366205,
-       "RELAX partitioned descriptive":0.1196402015693241,
-       "k (general descriptive)":1.977892771876671
-      },
-     "Node8":{
-       "General descriptive":0.140412283431793,
-       "MG94xREV with separate rates for branch sets":0.1091939823455765,
-       "Nucleotide GTR":0.1062201244057951,
-       "RELAX alternative":0.1284192265733904,
-       "RELAX null":0.1334227466998376,
-       "RELAX partitioned descriptive":0.1367904558404228,
-       "k (general descriptive)":2.206967022203622
-      },
-     "Node9":{
-       "General descriptive":0.02664133794298214,
-       "MG94xREV with separate rates for branch sets":0.02578742148415842,
-       "Nucleotide GTR":0.02567813733543303,
-       "RELAX alternative":0.02680940150436639,
-       "RELAX null":0.0273694783141817,
-       "RELAX partitioned descriptive":0.02747376898615263,
-       "k (general descriptive)":0.07343731037788495
-      },
-     "Pig":{
-       "General descriptive":0.210591346560755,
-       "MG94xREV with separate rates for branch sets":0.1903463787974325,
-       "Nucleotide GTR":0.1871390433004313,
-       "RELAX alternative":0.1974790507889271,
-       "RELAX null":0.2130024973755621,
-       "RELAX partitioned descriptive":0.2084407457285946,
-       "k (general descriptive)":1.581210670484469,
-       "original name":"Pig"
-      },
-     "Rat":{
-       "General descriptive":0.07157977734335202,
-       "MG94xREV with separate rates for branch sets":0.06709765698107663,
-       "Nucleotide GTR":0.06661490534189227,
-       "RELAX alternative":0.07252374836036582,
-       "RELAX null":0.0734705682786943,
-       "RELAX partitioned descriptive":0.0757525093290258,
-       "k (general descriptive)":1.316568267879453,
-       "original name":"Rat"
-      },
-     "RhMonkey":{
-       "General descriptive":0.003672848089716511,
-       "MG94xREV with separate rates for branch sets":0.003717350789869306,
-       "Nucleotide GTR":0.003778804730491441,
-       "RELAX alternative":0.003633278464154418,
-       "RELAX null":0.003661271320845124,
-       "RELAX partitioned descriptive":0.003625957794514879,
-       "k (general descriptive)":5.196295069596697,
-       "original name":"RhMonkey"
-      }
-    },
-   "attributes":{
-     "General descriptive":{
-       "attribute type":"branch length",
-       "display order":4
-      },
-     "MG94xREV with separate rates for branch sets":{
-       "attribute type":"branch length",
-       "display order":1
-      },
-     "Nucleotide GTR":{
-       "attribute type":"branch length",
-       "display order":0
-      },
-     "RELAX alternative":{
-       "attribute type":"branch length",
-       "display order":2
-      },
-     "RELAX null":{
-       "attribute type":"branch length",
-       "display order":3
-      },
-     "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":6945.892677835464,
-     "Log Likelihood":-3420.487593043145,
-     "Rate Distributions":{
-       "Shared":{
-         "0":{
-           "omega":2.201451464048879e-18,
-           "proportion":0.3073650505039141
-          },
-         "1":{
-           "omega":2.201451464048879e-18,
-           "proportion":0.2383891488636319
-          },
-         "2":{
-           "omega":2.201451281679838,
-           "proportion":0.4542458006324541
-          }
-        }
-      },
-     "display order":4,
-     "estimated parameters":51
-    },
-   "MG94xREV with separate rates for branch sets":{
-     "AIC-c":6987.566513560764,
-     "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":-3461.208406480981,
-     "Rate Distributions":{
-       "non-synonymous/synonymous rate ratio for *Reference*":        [
-[0.7685912547191639, 1] 
-        ],
-       "non-synonymous/synonymous rate ratio for *Test*":        [
-[1.603198088111489, 1] 
-        ]
-      },
-     "display order":1,
-     "estimated parameters":32
-    },
-   "Nucleotide GTR":{
-     "AIC-c":7112.857288723968,
-     "Equilibrium frequencies":      [
-[0.3592490842490842],
-      [0.181959706959707],
-      [0.240018315018315],
-      [0.2187728937728937] 
-      ],
-     "Log Likelihood":-3532.321213744258,
-     "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":0.2646800222727828,
-       "Substitution rate from nucleotide C to nucleotide G":0.4918071762416347,
-       "Substitution rate from nucleotide C to nucleotide T":1.028675134787727,
-       "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741
-      },
-     "display order":0,
-     "estimated parameters":24
-    },
-   "RELAX alternative":{
-     "AIC-c":6931.926773483473,
-     "Log Likelihood":-3429.236709163995,
-     "Rate Distributions":{
-       "Reference":{
-         "0":{
-           "omega":1.761161171239182e-19,
-           "proportion":0.2691773911207853
-          },
-         "1":{
-           "omega":1.762922332410267e-19,
-           "proportion":0.2692122656891806
-          },
-         "2":{
-           "omega":2.208286837998088,
-           "proportion":0.4616103431900341
-          }
-        },
-       "Test":{
-         "0":{
-           "omega":1.673670300056362e-44,
-           "proportion":0.2691773911207853
-          },
-         "1":{
-           "omega":1.677579612236672e-44,
-           "proportion":0.2692122656891806
-          },
-         "2":{
-           "omega":6.354762788556926,
-           "proportion":0.4616103431900341
-          }
-        }
-      },
-     "display order":2,
-     "estimated parameters":36
-    },
-   "RELAX null":{
-     "AIC-c":6946.648596594286,
-     "Log Likelihood":-3437.63727539638,
-     "Rate Distributions":{
-       "Reference":{
-         "0":{
-           "omega":1.408928936991542e-20,
-           "proportion":0.265244047162938
-          },
-         "1":{
-           "omega":1.410337865928411e-20,
-           "proportion":0.28512630848952
-          },
-         "2":{
-           "omega":3.213510017765925,
-           "proportion":0.4496296443475419
-          }
-        },
-       "Test":{
-         "0":{
-           "omega":1.408928936991542e-20,
-           "proportion":0.265244047162938
-          },
-         "1":{
-           "omega":1.410337865928411e-20,
-           "proportion":0.28512630848952
-          },
-         "2":{
-           "omega":3.213510017765925,
-           "proportion":0.4496296443475419
-          }
-        }
-      },
-     "display order":3,
-     "estimated parameters":35
-    },
-   "RELAX partitioned descriptive":{
-     "AIC-c":6937.049237937651,
-     "Log Likelihood":-3427.627954124649,
-     "Rate Distributions":{
-       "Reference":{
-         "0":{
-           "omega":0.1847557016619168,
-           "proportion":0.4766160247339328
-          },
-         "1":{
-           "omega":0.3367540359539261,
-           "proportion":0.3005513276312735
-          },
-         "2":{
-           "omega":4.272816072857538,
-           "proportion":0.2228326476347937
-          }
-        },
-       "Test":{
-         "0":{
-           "omega":1.127143149593234e-21,
-           "proportion":0.2367540589657237
-          },
-         "1":{
-           "omega":1.128270292740756e-21,
-           "proportion":0.2771164325302933
-          },
-         "2":{
-           "omega":6.023626417874829,
-           "proportion":0.4861295085039831
-          }
-        }
-      },
-     "display order":5,
-     "estimated parameters":40
-    }
-  },
- "input":{
-   "file name":"/tmp/tmpkgsdjj1d/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)"
-    }
-  },
- "runtime":"2.5.32",
- "test results":{
-   "LRT":16.80113246476958,
-   "p-value":4.150852429507523e-05,
-   "relaxation or intensification parameter":2.334214628944839
-  },
- "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":127
-    },
-   "Overall":{
-     "order":0,
-     "timer":396
-    },
-   "Preliminary model fitting":{
-     "order":1,
-     "timer":8
-    },
-   "RELAX alternative model fitting":{
-     "order":3,
-     "timer":103
-    },
-   "RELAX null model fitting":{
-     "order":4,
-     "timer":41
-    },
-   "RELAX partitioned descriptive":{
-     "order":5,
-     "timer":116
-    }
-  }
-}
\ No newline at end of file