Mercurial > repos > iuc > hyphy_sm19

changeset 15:23b9bd244670 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"
author iuc
date Fri, 18 Sep 2020 21:07:08 +0000
parents 40e9160dbbbb
children 2126c9e28ce6
files test-data/absrel-out1.json
diffstat 1 files changed, 407 insertions(+), 385 deletions(-) [+]
line wrap: on
line diff
--- a/test-data/absrel-out1.json	Fri Aug 21 15:27:13 2020 -0400
+++ b/test-data/absrel-out1.json	Fri Sep 18 21:07:08 2020 +0000
@@ -1,424 +1,253 @@
 {
  "analysis":{
-   "info":"aBSREL (Adaptive branch-site random effects likelihood)\n                            uses an adaptive random effects branch-site model framework\n                            to test whether each branch has evolved under positive selection,\n                            using a procedure which infers an optimal number of rate categories per branch.",
-   "version":"2.0",
-   "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353",
    "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
+   "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353. v2.2 adds support for multiple-hit models",
    "contact":"spond@temple.edu",
-   "requirements":"in-frame codon alignment and a phylogenetic tree"
-  },
- "input":{
-   "file name":"/tmp/tmpCAMqUO/job_working_directory/002/2602/working/absrel_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":-3531.96369518556,
-     "estimated parameters":24,
-     "AIC-c":7112.577796875186,
-     "Equilibrium frequencies":[
-      [0.3563279857397504],
-      [0.1837789661319073],
-      [0.2402852049910873],
-      [0.2196078431372549]
-      ],
-     "Rate Distributions":{
-       "Substitution rate from nucleotide A to nucleotide C":0.5474707834424497,
-       "Substitution rate from nucleotide A to nucleotide G":1,
-       "Substitution rate from nucleotide A to nucleotide T":0.2645731370379643,
-       "Substitution rate from nucleotide C to nucleotide G":0.4867482826410435,
-       "Substitution rate from nucleotide C to nucleotide T":1.018295973581558,
-       "Substitution rate from nucleotide G to nucleotide T":0.3026112531229544
-      },
-     "display order":0
-    },
-   "Baseline MG94xREV":{
-     "Log Likelihood":-3450.669934819203,
-     "estimated parameters":46,
-     "AIC-c":6995.711784065174,
-     "Equilibrium frequencies":[
-      [0.04787662253946073],
-      [0.03913388100305117],
-      [0.04844580322128512],
-      [0.0407178971288476],
-      [0.01817959331488358],
-      [0.01485982100934833],
-      [0.01839572120297191],
-      [0.01546129971531724],
-      [0.0190238172858878],
-      [0.01554988139098808],
-      [0.01924998172104109],
-      [0.01617929156565557],
-      [0.02798385246472159],
-      [0.02287372613761008],
-      [0.02831653817605838],
-      [0.02379958245776909],
-      [0.01680670574479072],
-      [0.01373763619452979],
-      [0.01700651207463693],
-      [0.01429369239710176],
-      [0.006381800954137531],
-      [0.005216421415661322],
-      [0.006457670922102578],
-      [0.00542756570877943],
-      [0.006678159032689796],
-      [0.005458661598138652],
-      [0.00675755225029668],
-      [0.00567961101013393],
-      [0.009823507779659469],
-      [0.008029638769211124],
-      [0.009940294440024354],
-      [0.008354653231583485],
-      [0.0329096029621651],
-      [0.02689998621179963],
-      [0.03330084840219455],
-      [0.02798881284619018],
-      [0.01249635346589736],
-      [0.01021439657952951],
-      [0.01264491622176376],
-      [0.01062784315018763],
-      [0.01307665913959002],
-      [0.01068873273724336],
-      [0.0132321208528494],
-      [0.01112137894012831],
-      [0.01923563996618058],
-      [0.01572302316926395],
-      [0.01946432265285621],
-      [0.01635944157725275],
-      [0.01977100255021048],
-      [0.02057127040149398],
-      [0.009184593415672956],
-      [0.007507396443725858],
-      [0.009293784349897772],
-      [0.007811272183233558],
-      [0.007856024926654371],
-      [0.009725369116048951],
-      [0.008174012048031599],
-      [0.01413784690564137],
-      [0.01155613719386138],
-      [0.01430592453757226],
-      [0.01202389319448819]
-      ],
-     "Rate Distributions":{
-       "Per-branch omega":{
-         "Mean":666666667.6064719,
-         "Median":1.103169534345197,
-         "2.5%":0,
-         "97.5%":10000000000
-        }
-      },
-     "display order":1
-    },
-   "Full adaptive model":{
-     "Log Likelihood":-3414.992415597899,
-     "estimated parameters":60,
-     "AIC-c":6954.031265689993,
-     "Rate Distributions":{
-      },
-     "display order":2
-    }
-  },
- "timers":{
-   "Overall":{
-     "timer":98,
-     "order":0
-    },
-   "Preliminary model fitting":{
-     "timer":0,
-     "order":1
-    },
-   "Baseline model fitting":{
-     "timer":1,
-     "order":2
-    },
-   "Complexity analysis":{
-     "timer":36,
-     "order":3
-    },
-   "Full adaptive model fitting":{
-     "timer":8,
-     "order":4
-    },
-   "Testing for selection":{
-     "timer":53,
-     "order":5
-    }
-  },
- "test results":{
-   "P-value threshold":0.05,
-   "tested":16,
-   "positive test results":3
-  },
- "tested":{
-   "0":{
-     "Pig":"test",
-     "Cow":"test",
-     "Node3":"test",
-     "Horse":"test",
-     "Cat":"test",
-     "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":"absrel.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]
-      ]
-    }
+   "info":"aBSREL (Adaptive branch-site random effects likelihood)\n                            uses an adaptive random effects branch-site model framework\n                            to test whether each branch has evolved under positive selection,\n                            using a procedure which infers an optimal number of rate categories per branch.",
+   "requirements":"in-frame codon alignment and a phylogenetic tree",
+   "version":"2.2"
   },
  "branch attributes":{
    "0":{
-     "Human":{
-       "original name":"Human",
-       "Nucleotide GTR":0,
-       "Baseline MG94xREV":0,
-       "Baseline MG94xREV omega ratio":1,
-       "Rate classes":1,
-       "Full adaptive model":0,
-       "Rate Distributions":[
-        [1, 1]
-        ],
+     "Baboon":{
+       "Baseline MG94xREV":0.001816807585564731,
+       "Baseline MG94xREV omega ratio":0,
+       "Corrected P-value":1,
+       "Full adaptive model":0.001810407118394509,
        "LRT":0,
-       "Uncorrected P-value":1,
-       "Corrected P-value":1
-      },
-     "Chimp":{
-       "original name":"Chimp",
-       "Nucleotide GTR":0.001818174796225333,
-       "Baseline MG94xREV":0.001839770270131542,
-       "Baseline MG94xREV omega ratio":10000000000,
-       "Rate classes":1,
-       "Full adaptive model":0.001845806111200226,
-       "Rate Distributions":[
-        [10000000000, 1]
+       "Nucleotide GTR":0.001678881906620672,
+       "Rate Distributions":        [
+[0, 1] 
         ],
-       "LRT":0.6362875427803374,
-       "Uncorrected P-value":0.303261123771571,
-       "Corrected P-value":1
-      },
-     "Baboon":{
-       "original name":"Baboon",
-       "Nucleotide GTR":0.001682034724848474,
-       "Baseline MG94xREV":0.001821072110941238,
-       "Baseline MG94xREV omega ratio":0,
-       "Rate classes":1,
-       "Full adaptive model":0.001808294153407354,
-       "Rate Distributions":[
-        [0, 1]
-        ],
-       "LRT":0,
-       "Uncorrected P-value":1,
-       "Corrected P-value":1
-      },
-     "RhMonkey":{
-       "original name":"RhMonkey",
-       "Nucleotide GTR":0.003775509884015639,
-       "Baseline MG94xREV":0.003671340584166445,
-       "Baseline MG94xREV omega ratio":10000000000,
        "Rate classes":1,
-       "Full adaptive model":0.003682180830540259,
-       "Rate Distributions":[
-        [10000000000, 1]
-        ],
-       "LRT":1.200615147074132,
-       "Uncorrected P-value":0.2192326116145807,
-       "Corrected P-value":1
-      },
-     "Cow":{
-       "original name":"Cow",
-       "Nucleotide GTR":0.248257545271419,
-       "Baseline MG94xREV":0.2535517510207829,
-       "Baseline MG94xREV omega ratio":1.957039676836281,
-       "Rate classes":2,
-       "Full adaptive model":0.3959632497370367,
-       "Rate Distributions":[
-        [0, 0.5384412409742189],
-        [10.58123012791267, 0.4615587590257811]
-        ],
-       "LRT":24.50128746473001,
-       "Uncorrected P-value":1.583131814197891e-06,
-       "Corrected P-value":2.533010902716626e-05
-      },
-     "Pig":{
-       "original name":"Pig",
-       "Nucleotide GTR":0.1872143003439852,
-       "Baseline MG94xREV":0.1913752025483544,
-       "Baseline MG94xREV omega ratio":1.354835319497051,
-       "Rate classes":1,
-       "Full adaptive model":0.1823079562415392,
-       "Rate Distributions":[
-        [1.270031670375847, 1]
-        ],
-       "LRT":0.5083013304356427,
-       "Uncorrected P-value":0.3278475069550038,
-       "Corrected P-value":1
-      },
-     "Horse":{
-       "original name":"Horse",
-       "Nucleotide GTR":0.2092211101976542,
-       "Baseline MG94xREV":0.2093433205074538,
-       "Baseline MG94xREV omega ratio":1.262933703792719,
-       "Rate classes":2,
-       "Full adaptive model":0.2696870893488891,
-       "Rate Distributions":[
-        [0, 0.5494326491453121],
-        [4.447670371762946, 0.4505673508546879]
-        ],
-       "LRT":9.839972152766677,
-       "Uncorrected P-value":0.002531289908698275,
-       "Corrected P-value":0.03543805872177586
+       "Uncorrected P-value":1,
+       "original name":"Baboon",
+       "rate at which 2 nucleotides are changed instantly within a single codon":0
       },
      "Cat":{
-       "original name":"Cat",
-       "Nucleotide GTR":0.2662269345134692,
-       "Baseline MG94xREV":0.2773733494290757,
-       "Baseline MG94xREV omega ratio":1.619113019542315,
+       "Baseline MG94xREV":0.2286001363527903,
+       "Baseline MG94xREV omega ratio":1.403298474422089,
+       "Corrected P-value":1,
+       "Full adaptive model":0.1219386838393392,
+       "LRT":1.644967676056694,
+       "Nucleotide GTR":0.265904547400163,
+       "Rate Distributions":        [
+[0.2130519766306851, 0.6352283641519592],
+        [2.628217450705319, 0.3647716358480408] 
+        ],
        "Rate classes":2,
-       "Full adaptive model":0.3637840333790108,
-       "Rate Distributions":[
-        [0.3427137549260186, 0.5775012741005606],
-        [6.025097508634321, 0.4224987258994394]
+       "Uncorrected P-value":0.171730764045231,
+       "original name":"Cat",
+       "rate at which 2 nucleotides are changed instantly within a single codon":0
+      },
+     "Chimp":{
+       "Baseline MG94xREV":0.001840311209746262,
+       "Baseline MG94xREV omega ratio":10000000000,
+       "Corrected P-value":1,
+       "Full adaptive model":0.001841979303044237,
+       "LRT":0.6159123786974305,
+       "Nucleotide GTR":0.001816713800925801,
+       "Rate Distributions":        [
+[10000000000, 1] 
+        ],
+       "Rate classes":1,
+       "Uncorrected P-value":0.3069983227523322,
+       "original name":"Chimp",
+       "rate at which 2 nucleotides are changed instantly within a single codon":0
+      },
+     "Cow":{
+       "Baseline MG94xREV":0.2070244948790512,
+       "Baseline MG94xREV omega ratio":2.153434974462683,
+       "Corrected P-value":0.5006146299996015,
+       "Full adaptive model":0.1241125417707662,
+       "LRT":4.898194538953248,
+       "Nucleotide GTR":0.2481512612523618,
+       "Rate Distributions":        [
+[0, 0.52318726440949],
+        [2.444056517734385, 0.47681273559051] 
         ],
-       "LRT":13.05292728184577,
-       "Uncorrected P-value":0.000499814517576469,
-       "Corrected P-value":0.007497217763647035
+       "Rate classes":2,
+       "Uncorrected P-value":0.03128841437497509,
+       "original name":"Cow",
+       "rate at which 2 nucleotides are changed instantly within a single codon":0
+      },
+     "Horse":{
+       "Baseline MG94xREV":0.190365915457708,
+       "Baseline MG94xREV omega ratio":1.182933895494305,
+       "Corrected P-value":1,
+       "Full adaptive model":0.0869489794025302,
+       "LRT":2.047309801283518,
+       "Nucleotide GTR":0.2090927256979082,
+       "Rate Distributions":        [
+[0, 0.5397658078247131],
+        [1.633257246666139, 0.4602341921752869] 
+        ],
+       "Rate classes":2,
+       "Uncorrected P-value":0.1382789032066179,
+       "original name":"Horse",
+       "rate at which 2 nucleotides are changed instantly within a single codon":0
+      },
+     "Human":{
+       "Baseline MG94xREV":0,
+       "Baseline MG94xREV omega ratio":1,
+       "Corrected P-value":1,
+       "Full adaptive model":0,
+       "LRT":0,
+       "Nucleotide GTR":0,
+       "Rate Distributions":        [
+[1, 1] 
+        ],
+       "Rate classes":1,
+       "Uncorrected P-value":1,
+       "original name":"Human",
+       "rate at which 2 nucleotides are changed instantly within a single codon":0.0006106118725184574
       },
      "Mouse":{
-       "original name":"Mouse",
-       "Nucleotide GTR":0.1181551390736968,
-       "Baseline MG94xREV":0.1220127721537473,
-       "Baseline MG94xREV omega ratio":0.5307054960008202,
+       "Baseline MG94xREV":0.1083167307250788,
+       "Baseline MG94xREV omega ratio":0.5108576904540283,
+       "Corrected P-value":1,
+       "Full adaptive model":0.1078010043714489,
+       "LRT":0,
+       "Nucleotide GTR":0.1181001275359051,
+       "Rate Distributions":        [
+[0.5087375113796073, 1] 
+        ],
        "Rate classes":1,
-       "Full adaptive model":0.1200052061883895,
-       "Rate Distributions":[
-        [0.5418818043457002, 1]
-        ],
-       "LRT":0,
        "Uncorrected P-value":1,
-       "Corrected P-value":1
-      },
-     "Rat":{
-       "original name":"Rat",
-       "Nucleotide GTR":0.06673994656462794,
-       "Baseline MG94xREV":0.06546903135094065,
-       "Baseline MG94xREV omega ratio":1.103169534345197,
-       "Rate classes":1,
-       "Full adaptive model":0.06894368446818594,
-       "Rate Distributions":[
-        [1.162844601638596, 1]
-        ],
-       "LRT":0.04180897168953379,
-       "Uncorrected P-value":0.4613906175252571,
-       "Corrected P-value":1
+       "original name":"Mouse",
+       "rate at which 2 nucleotides are changed instantly within a single codon":0.4244832903005548
       },
      "Node1":{
-       "Nucleotide GTR":0.2772613398768408,
-       "Baseline MG94xREV":0.2903229694372956,
-       "Baseline MG94xREV omega ratio":0.4389914526526448,
-       "Rate classes":2,
-       "Full adaptive model":0.3664538683295676,
-       "Rate Distributions":[
-        [0.1934444279004118, 0.7920338324503209],
-        [2.595458156723663, 0.2079661675496791]
+       "Baseline MG94xREV":0.2542393300501047,
+       "Baseline MG94xREV omega ratio":0.2997498382776075,
+       "Corrected P-value":1,
+       "Full adaptive model":0.2550466752020236,
+       "LRT":0,
+       "Nucleotide GTR":0.2767426965701868,
+       "Rate Distributions":        [
+[0.2932817609633239, 1] 
         ],
-       "LRT":1.095302853601424,
-       "Uncorrected P-value":0.232551772988317,
-       "Corrected P-value":1
+       "Rate classes":1,
+       "Uncorrected P-value":1,
+       "rate at which 2 nucleotides are changed instantly within a single codon":0.9114373463003921
       },
      "Node12":{
-       "Nucleotide GTR":0.01783922546179193,
-       "Baseline MG94xREV":0.01797212760838867,
-       "Baseline MG94xREV omega ratio":0.3712490894908597,
+       "Baseline MG94xREV":0.01400815185374474,
+       "Baseline MG94xREV omega ratio":0.2754467062829232,
+       "Corrected P-value":1,
+       "Full adaptive model":0.01437973904273591,
+       "LRT":0,
+       "Nucleotide GTR":0.01784721909304638,
+       "Rate Distributions":        [
+[0.3037614070859027, 1] 
+        ],
        "Rate classes":1,
-       "Full adaptive model":0.01648897148329989,
-       "Rate Distributions":[
-        [0.3341484726344874, 1]
-        ],
-       "LRT":0,
        "Uncorrected P-value":1,
-       "Corrected P-value":1
+       "rate at which 2 nucleotides are changed instantly within a single codon":0.5084909616267814
       },
      "Node2":{
-       "Nucleotide GTR":0.06619058539001231,
-       "Baseline MG94xREV":0.06580724801157116,
-       "Baseline MG94xREV omega ratio":0.6811307469311604,
-       "Rate classes":2,
-       "Full adaptive model":0.1259563484776556,
-       "Rate Distributions":[
-        [0, 0.902872882268449],
-        [33.80023214939837, 0.09712711773155103]
+       "Baseline MG94xREV":0.0400106272595141,
+       "Baseline MG94xREV omega ratio":0.116408812566168,
+       "Corrected P-value":1,
+       "Full adaptive model":0.03991940069030483,
+       "LRT":0,
+       "Nucleotide GTR":0.06613304839358287,
+       "Rate Distributions":        [
+[0.1193993042178124, 1] 
         ],
-       "LRT":7.670975764417562,
-       "Uncorrected P-value":0.007599562698001494,
-       "Corrected P-value":0.09119475237601793
+       "Rate classes":1,
+       "Uncorrected P-value":1,
+       "rate at which 2 nucleotides are changed instantly within a single codon":9.28646275825122
       },
      "Node3":{
-       "Nucleotide GTR":0.09883236156840018,
-       "Baseline MG94xREV":0.102749851157051,
-       "Baseline MG94xREV omega ratio":1.47449378631578,
-       "Rate classes":2,
-       "Full adaptive model":0.1389308407753113,
-       "Rate Distributions":[
-        [0, 0.7024206790833775],
-        [8.065310624699681, 0.2975793209166225]
+       "Baseline MG94xREV":0.08548068002443369,
+       "Baseline MG94xREV omega ratio":1.293385437932658,
+       "Corrected P-value":1,
+       "Full adaptive model":0.08590119038008139,
+       "LRT":0.1383887036890883,
+       "Nucleotide GTR":0.09881178513658169,
+       "Rate Distributions":        [
+[1.330576641567385, 1] 
         ],
-       "LRT":6.598417720076213,
-       "Uncorrected P-value":0.0131150962965953,
-       "Corrected P-value":0.1442660592625483
+       "Rate classes":1,
+       "Uncorrected P-value":0.4219212196398351,
+       "rate at which 2 nucleotides are changed instantly within a single codon":0.8390789546113498
       },
      "Node8":{
-       "Nucleotide GTR":0.1061134663636472,
-       "Baseline MG94xREV":0.110140333084973,
-       "Baseline MG94xREV omega ratio":1.896243438714738,
-       "Rate classes":2,
-       "Full adaptive model":0.2165540926910564,
-       "Rate Distributions":[
-        [1, 0.9077840705139004],
-        [33.32075865076668, 0.09221592948609958]
+       "Baseline MG94xREV":0.09463393920061362,
+       "Baseline MG94xREV omega ratio":1.862136443854597,
+       "Corrected P-value":1,
+       "Full adaptive model":0.0958035263641453,
+       "LRT":0.7150293976401372,
+       "Nucleotide GTR":0.1062333225692588,
+       "Rate Distributions":        [
+[1.883870769808856, 1] 
         ],
-       "LRT":7.97288393366216,
-       "Uncorrected P-value":0.006519360772582139,
-       "Corrected P-value":0.08475169004356781
+       "Rate classes":1,
+       "Uncorrected P-value":0.2893795680778183,
+       "rate at which 2 nucleotides are changed instantly within a single codon":0.512238843416092
       },
      "Node9":{
-       "Nucleotide GTR":0.02566719422260768,
-       "Baseline MG94xREV":0.02590165433349057,
-       "Baseline MG94xREV omega ratio":0.4071738826525522,
+       "Baseline MG94xREV":0.02846111726225027,
+       "Baseline MG94xREV omega ratio":0.4321055128385307,
+       "Corrected P-value":1,
+       "Full adaptive model":0.02810856974543091,
+       "LRT":0,
+       "Nucleotide GTR":0.02566185438854229,
+       "Rate Distributions":        [
+[0.4185836885800617, 1] 
+        ],
+       "Rate classes":1,
+       "Uncorrected P-value":1,
+       "rate at which 2 nucleotides are changed instantly within a single codon":0
+      },
+     "Pig":{
+       "Baseline MG94xREV":0.1782835053555321,
+       "Baseline MG94xREV omega ratio":1.275728452678247,
+       "Corrected P-value":1,
+       "Full adaptive model":0.1729188354138871,
+       "LRT":0.3324036585026988,
+       "Nucleotide GTR":0.1871760137183495,
+       "Rate Distributions":        [
+[1.235108129487059, 1] 
+        ],
        "Rate classes":1,
-       "Full adaptive model":0.02766629863085238,
-       "Rate Distributions":[
-        [0.4488424899910019, 1]
+       "Uncorrected P-value":0.3669120164240152,
+       "original name":"Pig",
+       "rate at which 2 nucleotides are changed instantly within a single codon":0.1143447431158695
+      },
+     "Rat":{
+       "Baseline MG94xREV":0.06315403896300904,
+       "Baseline MG94xREV omega ratio":0.8744850915248316,
+       "Corrected P-value":1,
+       "Full adaptive model":0.06408078523886611,
+       "LRT":0,
+       "Nucleotide GTR":0.0666364425850592,
+       "Rate Distributions":        [
+[0.8782045320352186, 1] 
         ],
-       "LRT":0,
+       "Rate classes":1,
        "Uncorrected P-value":1,
-       "Corrected P-value":1
+       "original name":"Rat",
+       "rate at which 2 nucleotides are changed instantly within a single codon":0.1346164190615118
+      },
+     "RhMonkey":{
+       "Baseline MG94xREV":0.003671939837747083,
+       "Baseline MG94xREV omega ratio":10000000000,
+       "Corrected P-value":1,
+       "Full adaptive model":0.003675047654636179,
+       "LRT":1.165062770327495,
+       "Nucleotide GTR":0.003777016173741061,
+       "Rate Distributions":        [
+[10000000000, 1] 
+        ],
+       "Rate classes":1,
+       "Uncorrected P-value":0.2236284592802686,
+       "original name":"RhMonkey",
+       "rate at which 2 nucleotides are changed instantly within a single codon":0
       }
     },
    "attributes":{
-     "original name":{
-       "attribute type":"node label",
-       "display order":-1
-      },
-     "Nucleotide GTR":{
-       "attribute type":"branch length",
-       "display order":0
-      },
      "Baseline MG94xREV":{
        "attribute type":"branch length",
        "display order":1
@@ -427,30 +256,223 @@
        "attribute type":"branch label",
        "display order":1
       },
-     "Rate classes":{
+     "Corrected P-value":{
        "attribute type":"branch label",
-       "display order":2
+       "display order":6
       },
      "Full adaptive model":{
        "attribute type":"branch length",
        "display order":2
       },
+     "LRT":{
+       "attribute type":"branch label",
+       "display order":4
+      },
+     "Nucleotide GTR":{
+       "attribute type":"branch length",
+       "display order":0
+      },
      "Rate Distributions":{
        "attribute type":"branch label",
        "display order":3
       },
-     "LRT":{
+     "Rate classes":{
        "attribute type":"branch label",
-       "display order":4
+       "display order":2
       },
      "Uncorrected P-value":{
        "attribute type":"branch label",
        "display order":5
       },
-     "Corrected P-value":{
+     "original name":{
+       "attribute type":"node label",
+       "display order":-1
+      },
+     "rate at which 2 nucleotides are changed instantly within a single codon":{
        "attribute type":"branch label",
-       "display order":6
+       "display order":7
       }
     }
+  },
+ "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":"absrel.filter.default"
+    }
+  },
+ "fits":{
+   "Baseline MG94xREV":{
+     "AIC-c":6983.763305606333,
+     "Equilibrium frequencies":      [
+[0.04875339327772683],
+      [0.03982858547830345],
+      [0.04946803524790992],
+      [0.04152216138298744],
+      [0.01811683453600613],
+      [0.01480036248560469],
+      [0.0183823965708893],
+      [0.01542969784826435],
+      [0.01894694796506697],
+      [0.01547851515238824],
+      [0.01922467805342367],
+      [0.01613668666381816],
+      [0.02832099415740372],
+      [0.02313654621336914],
+      [0.02873613184734657],
+      [0.02412034959764736],
+      [0.01662182431200483],
+      [0.01357902918971745],
+      [0.01686547203528639],
+      [0.01415643148428886],
+      [0.006176695005242439],
+      [0.005045987744654046],
+      [0.006267234867003878],
+      [0.005260551308914496],
+      [0.006459711194459957],
+      [0.005277194922783805],
+      [0.006554399593040238],
+      [0.005501589790395056],
+      [0.009655668202293983],
+      [0.007888099278638223],
+      [0.009797203904398108],
+      [0.008223514024394991],
+      [0.03326722643528176],
+      [0.02717732003095303],
+      [0.03375486749252685],
+      [0.02833294365668738],
+      [0.01236215156074466],
+      [0.01009913314808799],
+      [0.01254335971371867],
+      [0.01052856463184265],
+      [0.01292858539344675],
+      [0.0105618754683007],
+      [0.0131180965046964],
+      [0.01101098350431497],
+      [0.0193250328267319],
+      [0.01578738770911659],
+      [0.0196083049972345],
+      [0.01645869298147252],
+      [0.01962343746171723],
+      [0.02045785777700414],
+      [0.008926115885166477],
+      [0.007292098982657142],
+      [0.009056957588961733],
+      [0.007602170831388156],
+      [0.007626222986467745],
+      [0.009471947420992787],
+      [0.007950502328516303],
+      [0.01395367801862353],
+      [0.01139931439306339],
+      [0.01415821524731906],
+      [0.01188403168729233] 
+      ],
+     "Log Likelihood":-3427.720059001285,
+     "Rate Distributions":{
+       "Per-branch delta":{
+         "2.5%":0,
+         "97.5%":12.07373117808175,
+         "Mean":1.277646334033236,
+         "Median":0.4551223038316586
+        },
+       "Per-branch omega":{
+         "2.5%":0,
+         "97.5%":2.153434974462683,
+         "Mean":666666667.5119981,
+         "Median":1
+        }
+      },
+     "display order":1,
+     "estimated parameters":62
+    },
+   "Full adaptive model":{
+     "AIC-c":6972.859938351839,
+     "Log Likelihood":-3415.824749853321,
+     "Rate Distributions":{
+      },
+     "display order":2,
+     "estimated parameters":68
+    },
+   "Nucleotide GTR":{
+     "AIC-c":7112.857317645923,
+     "Equilibrium frequencies":      [
+[0.3592490842490842],
+      [0.181959706959707],
+      [0.240018315018315],
+      [0.2187728937728937] 
+      ],
+     "Log Likelihood":-3532.321228205235,
+     "Rate Distributions":{
+       "Substitution rate from nucleotide A to nucleotide C":0.5498703043473002,
+       "Substitution rate from nucleotide A to nucleotide G":1,
+       "Substitution rate from nucleotide A to nucleotide T":0.2646979624678532,
+       "Substitution rate from nucleotide C to nucleotide G":0.4921328068285813,
+       "Substitution rate from nucleotide C to nucleotide T":1.028960084526602,
+       "Substitution rate from nucleotide G to nucleotide T":0.3044365000595399
+      },
+     "display order":0,
+     "estimated parameters":24
+    }
+  },
+ "input":{
+   "file name":"/tmp/tmpx_42i6f0/job_working_directory/000/6/working/./absrel_input.fa",
+   "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":{
+   "P-value threshold":0.05,
+   "positive test results":0,
+   "tested":16
+  },
+ "tested":{
+   "0":{
+     "Baboon":"test",
+     "Cat":"test",
+     "Chimp":"test",
+     "Cow":"test",
+     "Horse":"test",
+     "Human":"test",
+     "Mouse":"test",
+     "Node1":"test",
+     "Node12":"test",
+     "Node2":"test",
+     "Node3":"test",
+     "Node8":"test",
+     "Node9":"test",
+     "Pig":"test",
+     "Rat":"test",
+     "RhMonkey":"test"
+    }
+  },
+ "timers":{
+   "Baseline model fitting":{
+     "order":2,
+     "timer":17
+    },
+   "Complexity analysis":{
+     "order":3,
+     "timer":110
+    },
+   "Full adaptive model fitting":{
+     "order":4,
+     "timer":20
+    },
+   "Overall":{
+     "order":0,
+     "timer":259
+    },
+   "Preliminary model fitting":{
+     "order":1,
+     "timer":0
+    },
+   "Testing for selection":{
+     "order":5,
+     "timer":112
+    }
   }
 }
\ No newline at end of file