--- a/test-data/busted-out2-1.json	Tue Oct 05 05:07:12 2021 +0000
+++ b/test-data/busted-out2-1.json	Sat Nov 27 11:27:32 2021 +0000
@@ -1,21 +1,21 @@
 {
  "Evidence Ratios":{
    "constrained":    [
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     ]
   },
  "analysis":{
@@ -26,94 +26,94 @@
    "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
    "version":"3.1"
   },
- "background":0,
+ "background":1,
  "branch attributes":{
    "0":{
      "B_FR_83_HXB2":{
-       "MG94xREV with separate rates for branch sets":0.01243274064118979,
+       "MG94xREV with separate rates for branch sets":0.0124534911696585,
        "Nucleotide GTR":0.01178680392701259,
-       "constrained":0.01256398347964253,
+       "constrained":0.0133332678009897,
        "original name":"B_FR_83_HXB2",
-       "unconstrained":0.01346367617740634
+       "unconstrained":0.01333097793183841
       },
      "B_US_83_RF":{
-       "MG94xREV with separate rates for branch sets":0.02861520854418918,
+       "MG94xREV with separate rates for branch sets":0.02861194347570897,
        "Nucleotide GTR":0.02637179869727959,
-       "constrained":0.02907713203932123,
+       "constrained":0.03221962988361129,
        "original name":"B_US_83_RF",
-       "unconstrained":0.03296423032791345
+       "unconstrained":0.03256468480049571
       },
      "B_US_86_JRFL":{
-       "MG94xREV with separate rates for branch sets":0.01913497611653954,
+       "MG94xREV with separate rates for branch sets":0.01907096200225401,
        "Nucleotide GTR":0.01766254318226218,
-       "constrained":0.01932498128977916,
+       "constrained":0.0202680273768515,
        "original name":"B_US_86_JRFL",
-       "unconstrained":0.02067264364489925
+       "unconstrained":0.02050998211592096
       },
      "B_US_90_WEAU160":{
-       "MG94xREV with separate rates for branch sets":0.02258152057123029,
+       "MG94xREV with separate rates for branch sets":0.0228124185259555,
        "Nucleotide GTR":0.0208836028381146,
-       "constrained":0.02318748492797678,
+       "constrained":0.02350080060535386,
        "original name":"B_US_90_WEAU160",
-       "unconstrained":0.02519768979779986
+       "unconstrained":0.03169576721730974
       },
      "D_CD_83_ELI":{
-       "MG94xREV with separate rates for branch sets":0.02096470337130958,
+       "MG94xREV with separate rates for branch sets":0.02096580136021227,
        "Nucleotide GTR":0.01905599613120992,
-       "constrained":0.02057807476219352,
+       "constrained":0.02146725583386667,
        "original name":"D_CD_83_ELI",
-       "unconstrained":0.02169258688744172
+       "unconstrained":0.02163106296740794
       },
      "D_CD_83_NDK":{
-       "MG94xREV with separate rates for branch sets":0.01034012674036274,
+       "MG94xREV with separate rates for branch sets":0.01029979658511127,
        "Nucleotide GTR":0.009776698714183414,
-       "constrained":0.0105101167818647,
+       "constrained":0.01035332290986223,
        "original name":"D_CD_83_NDK",
-       "unconstrained":0.01040169158313715
+       "unconstrained":0.01033266120816073
       },
      "D_CD_84_84ZR085":{
-       "MG94xREV with separate rates for branch sets":0.03124894063248942,
+       "MG94xREV with separate rates for branch sets":0.0311654066957857,
        "Nucleotide GTR":0.02822254903672137,
-       "constrained":0.03140845141419388,
+       "constrained":0.03323755030380494,
        "original name":"D_CD_84_84ZR085",
-       "unconstrained":0.03388014669054998
+       "unconstrained":0.03361093648063813
       },
      "D_UG_94_94UG114":{
-       "MG94xREV with separate rates for branch sets":0.0597102708893009,
+       "MG94xREV with separate rates for branch sets":0.05961647055090802,
        "Nucleotide GTR":0.05323070232023583,
-       "constrained":0.06218362660429492,
+       "constrained":0.06686538335493719,
        "original name":"D_UG_94_94UG114",
-       "unconstrained":0.06804948826756697
+       "unconstrained":0.06754551106553502
       },
      "Node1":{
-       "MG94xREV with separate rates for branch sets":0.02639559777106507,
+       "MG94xREV with separate rates for branch sets":0.02629484580500255,
        "Nucleotide GTR":0.02355240508560319,
-       "constrained":0.02779997592087442,
-       "unconstrained":0.02940126303315396
+       "constrained":0.02886080451868769,
+       "unconstrained":0.02913820563215103
       },
      "Node10":{
-       "MG94xREV with separate rates for branch sets":0.00193736936681532,
+       "MG94xREV with separate rates for branch sets":0.001918758877996093,
        "Nucleotide GTR":0.002230248981703367,
-       "constrained":0.001848018461605612,
-       "unconstrained":0.001859856019153286
+       "constrained":0.001805007516719466,
+       "unconstrained":0.001821173275343402
       },
      "Node2":{
-       "MG94xREV with separate rates for branch sets":0.003944601108756816,
+       "MG94xREV with separate rates for branch sets":0.003971092177388864,
        "Nucleotide GTR":0.003949360371801276,
-       "constrained":0.00346172246250584,
-       "unconstrained":0.002261770932022259
+       "constrained":0.002472638754288051,
+       "unconstrained":0.002387715711685514
       },
      "Node3":{
-       "MG94xREV with separate rates for branch sets":0.01136485742287924,
+       "MG94xREV with separate rates for branch sets":0.01135514370835145,
        "Nucleotide GTR":0.01048442975058683,
-       "constrained":0.01170820974676507,
-       "unconstrained":0.01401270546560647
+       "constrained":0.01356000749275525,
+       "unconstrained":0.01374972129226249
       },
      "Node9":{
-       "MG94xREV with separate rates for branch sets":0.005522231785763113,
+       "MG94xREV with separate rates for branch sets":0.005568732807049801,
        "Nucleotide GTR":0.004986123424162501,
-       "constrained":0.005522033787153708,
-       "unconstrained":0.005520113121560347
+       "constrained":0.00559084970119209,
+       "unconstrained":0.005669013080318036
       }
     },
    "attributes":{
@@ -149,29 +149,43 @@
   },
  "fits":{
    "Constrained model":{
-     "AIC-c":6398.612664722735,
-     "Log Likelihood":-3168.021928691643,
+     "AIC-c":6401.571605880178,
+     "Log Likelihood":-3164.403373999521,
      "Rate Distributions":{
+       "Background":{
+         "0":{
+           "omega":0.1702532607798455,
+           "proportion":0.8127334552706815
+          },
+         "1":{
+           "omega":0.2017838473060485,
+           "proportion":0.1774848965120759
+          },
+         "2":{
+           "omega":13.15236788524238,
+           "proportion":0.00978164821724258
+          }
+        },
        "Test":{
          "0":{
            "omega":0,
-           "proportion":0.6914129319908371
+           "proportion":0.8358903801628909
           },
          "1":{
-           "omega":0,
-           "proportion":0.07568144722655729
+           "omega":1,
+           "proportion":0.1436055877954064
           },
          "2":{
            "omega":1,
-           "proportion":0.2329056207826056
+           "proportion":0.02050403204170275
           }
         }
       },
      "display order":3,
-     "estimated parameters":31
+     "estimated parameters":36
     },
    "MG94xREV with separate rates for branch sets":{
-     "AIC-c":6408.899382280021,
+     "AIC-c":6410.490466219016,
      "Equilibrium frequencies":      [
 [0.07535940345366139],
       [0.01443006409728228],
@@ -235,14 +249,17 @@
       [0.0132120929750345],
       [0.01338903305480236] 
       ],
-     "Log Likelihood":-3176.217093030587,
+     "Log Likelihood":-3175.995949441886,
      "Rate Distributions":{
+       "non-synonymous/synonymous rate ratio for *background*":        [
+[0.2379324068936849, 1] 
+        ],
        "non-synonymous/synonymous rate ratio for *test*":        [
-[0.231720664913378, 1] 
+[0.1777604776475358, 1] 
         ]
       },
      "display order":1,
-     "estimated parameters":28
+     "estimated parameters":29
     },
    "Nucleotide GTR":{
      "AIC-c":6683.094244259512,
@@ -265,30 +282,44 @@
      "estimated parameters":21
     },
    "Unconstrained model":{
-     "AIC-c":6391.938375474656,
-     "Log Likelihood":-3163.666348620609,
+     "AIC-c":6400.149223170942,
+     "Log Likelihood":-3162.670820660715,
      "Rate Distributions":{
+       "Background":{
+         "0":{
+           "omega":0.1679188282558003,
+           "proportion":0.8207520434237199
+          },
+         "1":{
+           "omega":0.2120937673953722,
+           "proportion":0.1693698006934513
+          },
+         "2":{
+           "omega":13.84252711122189,
+           "proportion":0.00987815588282877
+          }
+        },
        "Test":{
          "0":{
-           "omega":0.1490485393860332,
-           "proportion":0.02658974082564446
+           "omega":0.08367159828032572,
+           "proportion":0.9533274940567786
           },
          "1":{
-           "omega":0.169565784922581,
-           "proportion":0.9641001770967245
+           "omega":0.2493792697064242,
+           "proportion":0.03716922067476962
           },
          "2":{
-           "omega":15.09387961636913,
-           "proportion":0.009310082077631076
+           "omega":34.20463703717275,
+           "proportion":0.009503285268451747
           }
         }
       },
      "display order":2,
-     "estimated parameters":32
+     "estimated parameters":37
     }
   },
  "input":{
-   "file name":"/tmp/tmpfqvtss8b/job_working_directory/000/5/working/./input.nex",
+   "file name":"/tmp/tmpfzf3u9m4/job_working_directory/000/2/working/./input.nex",
    "number of sequences":8,
    "number of sites":440,
    "partition count":1,
@@ -297,42 +328,42 @@
     }
   },
  "test results":{
-   "LRT":8.711160142067456,
-   "p-value":0.006417496108925114
+   "LRT":3.465106677611402,
+   "p-value":0.08841616008911996
   },
  "tested":{
    "0":{
-     "B_FR_83_HXB2":"test",
-     "B_US_83_RF":"test",
-     "B_US_86_JRFL":"test",
+     "B_FR_83_HXB2":"background",
+     "B_US_83_RF":"background",
+     "B_US_86_JRFL":"background",
      "B_US_90_WEAU160":"test",
-     "D_CD_83_ELI":"test",
-     "D_CD_83_NDK":"test",
-     "D_CD_84_84ZR085":"test",
-     "D_UG_94_94UG114":"test",
-     "Node1":"test",
-     "Node10":"test",
-     "Node2":"test",
-     "Node3":"test",
-     "Node9":"test"
+     "D_CD_83_ELI":"background",
+     "D_CD_83_NDK":"background",
+     "D_CD_84_84ZR085":"background",
+     "D_UG_94_94UG114":"background",
+     "Node1":"background",
+     "Node10":"background",
+     "Node2":"background",
+     "Node3":"background",
+     "Node9":"background"
     }
   },
  "timers":{
    "Constrained BUSTED model fitting":{
      "order":3,
-     "timer":23
+     "timer":14
     },
    "Overall":{
      "order":0,
-     "timer":133
+     "timer":60
     },
    "Preliminary model fitting":{
      "order":1,
-     "timer":4
+     "timer":3
     },
    "Unconstrained BUSTED model fitting":{
      "order":2,
-     "timer":105
+     "timer":40
     }
   }
 }
\ No newline at end of file