1{
2 "analysis":{
3   "info":"This analysis applies the Muse Gaut 94 (MG94) model with the GTR nucleotide rate component \n    to estimate the single dN/dS ratio for the alignment, and report its confidence intervals derived using profile likelihood.\n    There is an option to select a subset of branches for estimation, in which case a separate omega is estimated for the selected branches.\n    ",
4   "version":"0.1",
5   "citation":"A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome (1994). _Mol Biol Evol_ 11 (5): 715-724",
6   "authors":"Sergei L Kosakovsky Pond",
7   "contact":"spond@temple.edu",
8   "requirements":"in-frame codon alignment and a phylogenetic tree. Multiple partitions with a NEXUS file also supported"
9  },
10 "fits":{
11   "Nucleotide GTR":{
12     "Log Likelihood":-3531.963655447697,
13     "estimated parameters":24,
14     "AIC-c":7112.142172130845,
15     "Equilibrium frequencies":[
16      [0.3563279857397504],
17      [0.1837789661319073],
18      [0.2402852049910873],
19      [0.2196078431372549]
20      ],
21     "Rate Distributions":{
22       "Substitution rate from nucleotide A to nucleotide C":0.5482529321972486,
23       "Substitution rate from nucleotide A to nucleotide G":1,
24       "Substitution rate from nucleotide A to nucleotide T":0.264805832733209,
25       "Substitution rate from nucleotide C to nucleotide G":0.4876106791881865,
26       "Substitution rate from nucleotide C to nucleotide T":1.019842357841139,
27       "Substitution rate from nucleotide G to nucleotide T":0.3027177206743494
28      },
29     "display order":0
30    },
31   "Global MG94xREV":{
32     "Log Likelihood":-3466.725353220038,
33     "estimated parameters":31,
34     "AIC-c":6996.530140607651,
35     "Equilibrium frequencies":[
36      [0.04785168648208005],
37      [0.03911346079312019],
38      [0.04842054060317301],
39      [0.04069665666515385],
40      [0.01817010744778396],
41      [0.01485205303123071],
42      [0.01838611113045968],
43      [0.01545321970309948],
44      [0.0190138898893362],
45      [0.01554175184587827],
46      [0.01923992433904378],
47      [0.01617083546230154],
48      [0.02796925133965702],
49      [0.02286176927319543],
50      [0.02830174586718859],
51      [0.02378714529482007],
52      [0.01687870337957799],
53      [0.01379647304851128],
54      [0.01707935503225849],
55      [0.01435491300079667],
56      [0.006409133648843443],
57      [0.005238757839512795],
58      [0.006485324528555602],
59      [0.005450807083377185],
60      [0.006706760641638982],
61      [0.005482034985409045],
62      [0.006786489669196017],
63      [0.005703931360295163],
64      [0.009865581170012171],
65      [0.008064021368173151],
66      [0.009982861811889655],
67      [0.008390428826966174],
68      [0.03287895020631181],
69      [0.02687490503171972],
70      [0.033269810543681],
71      [0.0279627207822247],
72      [0.01248470225271473],
73      [0.01020486315060615],
74      [0.01263311863778268],
75      [0.01061792547971484],
76      [0.01306446616325414],
77      [0.01067875601941112],
78      [0.01321977470017749],
79      [0.01111100011404158],
80      [0.01921770557551369],
81      [0.01570834862514353],
82      [0.01944616295744266],
83      [0.01634417558076203],
84      [0.01975257768318274],
85      [0.02055210293142003],
86      [0.009176034326710849],
87      [0.007500393094996483],
88      [0.00928511773266342],
89      [0.007803986567571961],
90      [0.00784869593340758],
91      [0.009716299514778986],
92      [0.008166387662818644],
93      [0.01412467213650941],
94      [0.01154535713247913],
95      [0.01429258425298098],
96      [0.01201267864744234]
97      ],
98     "Rate Distributions":{
99       "0":[
100        [0.996924216533022, 1]
101        ]
102      },
103     "display order":1
104    },
105   "omega":{
106     "non-synonymous/synonymous rate ratio for *test*":{
107       "LB":0.9083129274311988,
108       "MLE":0.996924216533022,
109       "UB":1.089831238806418
110      }
111    }
112  },
113 "timers":{
114   "Total time":{
115     "timer":9,
116     "order":0
117    }
118  },
119 "tested":{
120   "0":{
121     "PIG":"test",
122     "COW":"test",
123     "Node3":"test",
124     "HORSE":"test",
125     "CAT":"test",
126     "Node2":"test",
127     "RHMONKEY":"test",
128     "BABOON":"test",
129     "Node9":"test",
130     "HUMAN":"test",
131     "CHIMP":"test",
132     "Node12":"test",
133     "Node8":"test",
134     "Node1":"test",
135     "RAT":"test",
136     "MOUSE":"test"
137    }
138  },
139 "input":{
140   "file name":"/Users/sergei/Development/hyphy-develop/tests/hbltests/data/CD2.nex",
141   "number of sequences":10,
142   "number of sites":187,
143   "partition count":1,
144   "trees":{
145     "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)"
146    }
147  },
148 "data partitions":{
149   "0":{
150     "name":"single_omega.filter.default",
151     "coverage":[
152      [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]
153      ]
154    }
155  },
156 "branch attributes":{
157   "0":{
158     "HUMAN":{
159       "original name":"HUMAN",
160       "Nucleotide GTR":0,
161       "Global MG94xREV":0
162      },
163     "CHIMP":{
164       "original name":"CHIMP",
165       "Nucleotide GTR":0.001819409505498532,
166       "Global MG94xREV":0.001830313020856732
167      },
168     "BABOON":{
169       "original name":"BABOON",
170       "Nucleotide GTR":0.001682207148475542,
171       "Global MG94xREV":0.001771862052542395
172      },
173     "RHMONKEY":{
174       "original name":"RHMONKEY",
175       "Nucleotide GTR":0.003775704995533204,
176       "Global MG94xREV":0.003718656169374045
177      },
178     "COW":{
179       "original name":"COW",
180       "Nucleotide GTR":0.248080655963153,
181       "Global MG94xREV":0.2481607489060679
182      },
183     "PIG":{
184       "original name":"PIG",
185       "Nucleotide GTR":0.1872739929226571,
186       "Global MG94xREV":0.1926123650858078
187      },
188     "HORSE":{
189       "original name":"HORSE",
190       "Nucleotide GTR":0.2089812616389708,
191       "Global MG94xREV":0.2112629012484836
192      },
193     "CAT":{
194       "original name":"CAT",
195       "Nucleotide GTR":0.2661351909060677,
196       "Global MG94xREV":0.2736352730879313
197      },
198     "MOUSE":{
199       "original name":"MOUSE",
200       "Nucleotide GTR":0.118210375708526,
201       "Global MG94xREV":0.1201852318281372
202      },
203     "RAT":{
204       "original name":"RAT",
205       "Nucleotide GTR":0.06676444909719663,
206       "Global MG94xREV":0.06704007343298489
207      },
208     "Node1":{
209       "Nucleotide GTR":0.2770985915795256,
210       "Global MG94xREV":0.2845062298344296
211      },
212     "Node12":{
213       "Nucleotide GTR":0.01784661013269995,
214       "Global MG94xREV":0.01788749017420944
215      },
216     "Node2":{
217       "Nucleotide GTR":0.06621080281260251,
218       "Global MG94xREV":0.06443131939831334
219      },
220     "Node3":{
221       "Nucleotide GTR":0.09881880264894725,
222       "Global MG94xREV":0.1016468208139953
223      },
224     "Node8":{
225       "Nucleotide GTR":0.1061558244712728,
226       "Global MG94xREV":0.1093725943478251
227      },
228     "Node9":{
229       "Nucleotide GTR":0.02566698049270639,
230       "Global MG94xREV":0.02593408269150705
231      }
232    },
233   "attributes":{
234     "original name":{
235       "attribute type":"node label",
236       "display order":-1
237      },
238     "Nucleotide GTR":{
239       "attribute type":"branch length",
240       "display order":0
241      },
242     "Global MG94xREV":{
243       "attribute type":"branch length",
244       "display order":1
245      }
246    }
247  }
248}