--- a/test-data/prime-out1.json	Thu Mar 02 15:02:12 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,391 +0,0 @@
-{
- "MLE":{
-   "content":{
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-      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
-      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
-      [7.592268336906083, 0, 0.5357744224661302, -5.63867473098278, -5.638674842181149, 1, -0.06122935182163709, 1, -5.638674730981298, -0.06122935182163709, 1, -5.638674730981298, -0.06122935182163709, 1, -5.638674730981298, -0.06122935182163709, 1, -5.638674730981298, -0.06122935182163709, 1, -5.638674730981298] 
-      ]
-    },
-   "headers":    [
-["alpha;", "Synonymous substitution rate at a site"],
-    ["β", "Log of property independent non-synonymous rate a site"],
-    ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"],
-    ["PRIME LogL", "Site Log-likelihood under the PRIME model"],
-    ["FEL LogL", "Site Log-likelihood under the FEL model"],
-    ["p-value", "Omnibus p-value (any property is important)"],
-    ["λ1", "Importance for Factor I bipolar"],
-    ["p1", "p-value for non-zero effect of Factor I bipolar"],
-    ["LogL1", "Log likelihood when there is no effect of Factor I bipolar"],
-    ["λ2", "Importance for Factor II secondary structure"],
-    ["p2", "p-value for non-zero effect of Factor II secondary structure"],
-    ["LogL2", "Log likelihood when there is no effect of Factor II secondary structure"],
-    ["λ3", "Importance for Factor III volume"],
-    ["p3", "p-value for non-zero effect of Factor III volume"],
-    ["LogL3", "Log likelihood when there is no effect of Factor III volume"],
-    ["λ4", "Importance for Factor IV composition"],
-    ["p4", "p-value for non-zero effect of Factor IV composition"],
-    ["LogL4", "Log likelihood when there is no effect of Factor IV composition"],
-    ["λ5", "Importance for Factor V charge"],
-    ["p5", "p-value for non-zero effect of Factor V charge"],
-    ["LogL5", "Log likelihood when there is no effect of Factor V charge"] 
-    ]
-  },
- "analysis":{
-   "authors":"Sergei L. Kosakovsky Pond",
-   "citation":"TBD",
-   "contact":"spond@temple.edu",
-   "info":"PRIME (PRoperty Informed Model of Evolution). Given a set of N amino-acid properties,\n    fit a site-level model where non-synonymous rates depend on how much a non-synonymous substitution changes the \n    properties of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )- lambda_2 * diff_2 (X,Y) -...).\n    When lambda_k > 0, changes in property k are disfavored and when lambda_k < 0 -- they are promoted.\n    At each site, N tests are performed\n    A subset of branches can be selected\n    for testing as well, in which case an additional (nuisance) parameter will be\n    inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n    for recombination - aware analysis.\n    ",
-   "requirements":"in-frame codon alignment and a phylogenetic tree",
-   "version":"0.0.1"
-  },
- "branch attributes":{
-   "0":{
-     "CHICKEN_CK_160_2005":{
-       "Global MG94xREV":0.006875905528136641,
-       "Nucleotide GTR":0.006740765844759078,
-       "original name":"CHICKEN_CK_160_2005"
-      },
-     "CHICKEN_HEBEI_326_2005":{
-       "Global MG94xREV":0.03000509055831138,
-       "Nucleotide GTR":0.02817726192677478,
-       "original name":"CHICKEN_HEBEI_326_2005"
-      },
-     "CHICKEN_HONGKONG_915_97":{
-       "Global MG94xREV":0,
-       "Nucleotide GTR":0,
-       "original name":"CHICKEN_HONGKONG_915_97"
-      },
-     "CK_HK_WF157_2003":{
-       "Global MG94xREV":0,
-       "Nucleotide GTR":0,
-       "original name":"CK_HK_WF157_2003"
-      },
-     "GOOSE_HONGKONG_W355_97":{
-       "Global MG94xREV":0,
-       "Nucleotide GTR":0,
-       "original name":"GOOSE_HONGKONG_W355_97"
-      },
-     "GOOSE_SHANTOU_2216_2005":{
-       "Global MG94xREV":0.008912012248907763,
-       "Nucleotide GTR":0.007985902570718373,
-       "original name":"GOOSE_SHANTOU_2216_2005"
-      },
-     "HONGKONG_1_538_97":{
-       "Global MG94xREV":0,
-       "Nucleotide GTR":0,
-       "original name":"HONGKONG_1_538_97"
-      },
-     "HONGKONG_1_97_98":{
-       "Global MG94xREV":0.02020234274992877,
-       "Nucleotide GTR":0.02001220163799822,
-       "original name":"HONGKONG_1_97_98"
-      },
-     "HUMAN_VIETNAM_3062_2004":{
-       "Global MG94xREV":0,
-       "Nucleotide GTR":0,
-       "original name":"HUMAN_VIETNAM_3062_2004"
-      },
-     "HUMAN_VIETNAM_CL105_2005":{
-       "Global MG94xREV":0.006025788919462983,
-       "Nucleotide GTR":0.005802088014335368,
-       "original name":"HUMAN_VIETNAM_CL105_2005"
-      },
-     "MALLARD_VIETNAM_16_2003":{
-       "Global MG94xREV":0,
-       "Nucleotide GTR":0,
-       "original name":"MALLARD_VIETNAM_16_2003"
-      },
-     "Node10":{
-       "Global MG94xREV":0,
-       "Nucleotide GTR":0
-      },
-     "Node11":{
-       "Global MG94xREV":0,
-       "Nucleotide GTR":0
-      },
-     "Node13":{
-       "Global MG94xREV":0,
-       "Nucleotide GTR":0
-      },
-     "Node17":{
-       "Global MG94xREV":0,
-       "Nucleotide GTR":0
-      },
-     "Node18":{
-       "Global MG94xREV":0,
-       "Nucleotide GTR":0
-      },
-     "Node19":{
-       "Global MG94xREV":0.004922199772633382,
-       "Nucleotide GTR":0.005534464552270369
-      },
-     "Node2":{
-       "Global MG94xREV":0.006872306486383904,
-       "Nucleotide GTR":0.006718147482064949
-      },
-     "Node23":{
-       "Global MG94xREV":0,
-       "Nucleotide GTR":0
-      },
-     "Node24":{
-       "Global MG94xREV":0,
-       "Nucleotide GTR":0
-      },
-     "Node25":{
-       "Global MG94xREV":0.0008268367968756879,
-       "Nucleotide GTR":0.0009189593587976459
-      },
-     "Node3":{
-       "Global MG94xREV":0,
-       "Nucleotide GTR":0
-      },
-     "Node4":{
-       "Global MG94xREV":0.002648185777377607,
-       "Nucleotide GTR":0.00251461257430795
-      },
-     "Node5":{
-       "Global MG94xREV":0.003268514528883674,
-       "Nucleotide GTR":0.003965274251091903
-      },
-     "Node7":{
-       "Global MG94xREV":0.005023432525711092,
-       "Nucleotide GTR":0.004793454999477672
-      },
-     "Node9":{
-       "Global MG94xREV":0.01391813691986412,
-       "Nucleotide GTR":0.01351408611669037
-      },
-     "PEREGRINEFALCON_HK_D0028_2004":{
-       "Global MG94xREV":0.006920710269269024,
-       "Nucleotide GTR":0.006722811033712868,
-       "original name":"PEREGRINEFALCON_HK_D0028_2004"
-      },
-     "SWINE_ANHUI_1_2004":{
-       "Global MG94xREV":0.01018798286684916,
-       "Nucleotide GTR":0.009150633137551082,
-       "original name":"SWINE_ANHUI_1_2004"
-      }
-    },
-   "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] 
-      ],
-     "name":"prime.filter.default"
-    }
-  },
- "fits":{
-   "Global MG94xREV":{
-     "AIC-c":647.6795207053656,
-     "Equilibrium frequencies":      [
-[0.04488063522282697],
-      [0.02743154763030629],
-      [0.03260676907658289],
-      [0.05361444334761576],
-      [0.01878621141548667],
-      [0.0114823431236735],
-      [0.01364859597925394],
-      [0.02244202343953587],
-      [0.00898846188937465],
-      [0.005493848721556544],
-      [0.006530315351495689],
-      [0.01073762388516669],
-      [0.04007728102844568],
-      [0.02449568367218243],
-      [0.02911702655775225],
-      [0.04787635251947601],
-      [0.02154103095825152],
-      [0.01316611972632322],
-      [0.01565003299619046],
-      [0.02573293310637029],
-      [0.009016680795182521],
-      [0.005511096433290134],
-      [0.006550817007515099],
-      [0.01077133421300087],
-      [0.004314126457096238],
-      [0.002636842477907016],
-      [0.003134307802358531],
-      [0.005153658975191914],
-      [0.01923560009946569],
-      [0.01175701452767408],
-      [0.01397508674685076],
-      [0.02297886352699522],
-      [0.03843194498464033],
-      [0.02349003582808618],
-      [0.02792165371671785],
-      [0.04591083274306419],
-      [0.01608690786137961],
-      [0.00983249851595989],
-      [0.0116874925496928],
-      [0.01921743321791434],
-      [0.00769695150511784],
-      [0.004704463089092132],
-      [0.005592004637968804],
-      [0.00919478452948895],
-      [0.03431876246786721],
-      [0.02097601254029597],
-      [0.02493333610872543],
-      [0.04099722156245031],
-      [0.006131000492593795],
-      [0.01198292502502543],
-      [0.004198752217504174],
-      [0.002566324448628536],
-      [0.003050485878513492],
-      [0.005015832814718212],
-      [0.001227885122343091],
-      [0.001459537288103269],
-      [0.002399878352343215],
-      [0.008957344771016727],
-      [0.00547482958980595],
-      [0.006507708080284218],
-      [0.01070045135026252] 
-      ],
-     "Log Likelihood":-277.7176481414617,
-     "Rate Distributions":{
-       "non-synonymous/synonymous rate ratio for *test*":        [
-[0.4074296362572946, 1] 
-        ]
-      },
-     "display order":1,
-     "estimated parameters":43
-    },
-   "Nucleotide GTR":{
-     "AIC-c":658.4548031196325,
-     "Equilibrium frequencies":      [
-[0.3543689320388349],
-      [0.1790722761596548],
-      [0.2076591154261057],
-      [0.2588996763754045] 
-      ],
-     "Log Likelihood":-292.5311130078037,
-     "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,
-       "Substitution rate from nucleotide C to nucleotide G":0,
-       "Substitution rate from nucleotide C to nucleotide T":1.816257034982832,
-       "Substitution rate from nucleotide G to nucleotide T":0
-      },
-     "display order":0,
-     "estimated parameters":36
-    }
-  },
- "input":{
-   "file name":"/Users/sergei/Development/tools-iuc/tools/hyphy/test-data/prime-in1.fa",
-   "number of sequences":13,
-   "number of sites":50,
-   "partition count":1,
-   "trees":{
-     "0":"(((((CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516)Node7:0.002095219592954275)Node5:0.003887237703073042)Node4:0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-1,(GOOSE_HONGKONG_W355_97:-1)Node13:0.002899766890966483)Node11:0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716)Node10:0.000182535836694054,HONGKONG_1_538_97:-1)Node9:0.02096173714686362)Node3:0.003130608143291779,(((GOOSE_SHANTOU_2216_2005:0.006207842095177651)Node19:0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232)Node18:0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774)Node17:0.004655295319725731)Node2:0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001)Node25:0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184)Node24:0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072)Node23:0.0004125980823087554,CHICKEN_CK_160_2005:0.006168335080088849)"
-    }
-  },
- "tested":{
-   "0":{
-     "CHICKEN_CK_160_2005":"test",
-     "CHICKEN_HEBEI_326_2005":"test",
-     "CHICKEN_HONGKONG_915_97":"test",
-     "CK_HK_WF157_2003":"test",
-     "GOOSE_HONGKONG_W355_97":"test",
-     "GOOSE_SHANTOU_2216_2005":"test",
-     "HONGKONG_1_538_97":"test",
-     "HONGKONG_1_97_98":"test",
-     "HUMAN_VIETNAM_3062_2004":"test",
-     "HUMAN_VIETNAM_CL105_2005":"test",
-     "MALLARD_VIETNAM_16_2003":"test",
-     "Node10":"test",
-     "Node11":"test",
-     "Node13":"test",
-     "Node17":"test",
-     "Node18":"test",
-     "Node19":"test",
-     "Node2":"test",
-     "Node23":"test",
-     "Node24":"test",
-     "Node25":"test",
-     "Node3":"test",
-     "Node4":"test",
-     "Node5":"test",
-     "Node7":"test",
-     "Node9":"test",
-     "PEREGRINEFALCON_HK_D0028_2004":"test",
-     "SWINE_ANHUI_1_2004":"test"
-    }
-  },
- "timers":{
-   "Model fitting":{
-     "order":1,
-     "timer":3
-    },
-   "PRIME analysis":{
-     "order":2,
-     "timer":86
-    },
-   "Total time":{
-     "order":0,
-     "timer":89
-    }
-  }
-}
\ No newline at end of file