Mercurial > repos > iuc > hyphy_fubar

comparison test-data/relax-out1.json @ 33:55a45d4c31dc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author iuc
date Wed, 30 Mar 2022 00:18:55 +0000
parents cd41e7a4d35f
children
comparison
equal deleted inserted replaced
32:90e57f65ddd9 33:55a45d4c31dc
1 { 1 {
2 "analysis":0, 2 "analysis":0,
3 "branch attributes":{ 3 "branch attributes":{
4 "0":{ 4 "0":{
5 "Baboon":{ 5 "Baboon":{
6 "General descriptive":0.001858767762813579, 6 "General descriptive":0.001859058366368826,
7 "MG94xREV with separate rates for branch sets":0.001769472024099301, 7 "MG94xREV with separate rates for branch sets":0.001769294089885709,
8 "Nucleotide GTR":0.001680040630127455, 8 "Nucleotide GTR":0.001685167654714891,
9 "RELAX alternative":0.001872256662230973, 9 "RELAX alternative":0.001873708670384941,
10 "RELAX null":0.001855569334462731, 10 "RELAX null":0.001859167714920677,
11 "RELAX partitioned descriptive":0.001898170574782418, 11 "RELAX partitioned descriptive":0.001898817195216417,
12 "k (general descriptive)":0.09971581394819819, 12 "k (general descriptive)":0.09969742933359635,
13 "original name":"Baboon" 13 "original name":"Baboon"
14 }, 14 },
15 "Cat":{ 15 "Cat":{
16 "General descriptive":0.3644803308678196, 16 "General descriptive":0.3650161006190072,
17 "MG94xREV with separate rates for branch sets":0.2796030091674721, 17 "MG94xREV with separate rates for branch sets":0.2796018473093496,
18 "Nucleotide GTR":0.2660909938917123, 18 "Nucleotide GTR":0.2660536011315811,
19 "RELAX alternative":0.3689219388980864, 19 "RELAX alternative":0.3685874431614762,
20 "RELAX null":0.3256077554105627, 20 "RELAX null":0.3167334440346762,
21 "RELAX partitioned descriptive":0.3717219559832593, 21 "RELAX partitioned descriptive":0.3719472357609613,
22 "k (general descriptive)":2.314507643873676, 22 "k (general descriptive)":2.319877215422834,
23 "original name":"Cat" 23 "original name":"Cat"
24 }, 24 },
25 "Chimp":{ 25 "Chimp":{
26 "General descriptive":0.001848680051431209, 26 "General descriptive":0.001895983937468787,
27 "MG94xREV with separate rates for branch sets":0.001825434296531533, 27 "MG94xREV with separate rates for branch sets":0.001826027667597702,
28 "Nucleotide GTR":0.001818373670119325, 28 "Nucleotide GTR":0.001820258053351119,
29 "RELAX alternative":0.001831703934281931, 29 "RELAX alternative":0.001831530791728368,
30 "RELAX null":0.00183525802483954, 30 "RELAX null":0.001834052740714585,
31 "RELAX partitioned descriptive":0.001832717232153088, 31 "RELAX partitioned descriptive":0.001832682515795942,
32 "k (general descriptive)":5.261186652622472, 32 "k (general descriptive)":5.158328270628251,
33 "original name":"Chimp" 33 "original name":"Chimp"
34 }, 34 },
35 "Cow":{ 35 "Cow":{
36 "General descriptive":0.3733627618450006, 36 "General descriptive":0.3737128696500712,
37 "MG94xREV with separate rates for branch sets":0.2520490246808783, 37 "MG94xREV with separate rates for branch sets":0.2521304147607955,
38 "Nucleotide GTR":0.2481025999892287, 38 "Nucleotide GTR":0.2480198736772598,
39 "RELAX alternative":0.342739998512865, 39 "RELAX alternative":0.3426997068768813,
40 "RELAX null":0.2948256709356563, 40 "RELAX null":0.2931467439343907,
41 "RELAX partitioned descriptive":0.3466331923230422, 41 "RELAX partitioned descriptive":0.3469082289876269,
42 "k (general descriptive)":2.846155982935764, 42 "k (general descriptive)":2.852150041266453,
43 "original name":"Cow" 43 "original name":"Cow"
44 }, 44 },
45 "Horse":{ 45 "Horse":{
46 "General descriptive":0.2802176313870697, 46 "General descriptive":0.2804279827409984,
47 "MG94xREV with separate rates for branch sets":0.2158304510870495, 47 "MG94xREV with separate rates for branch sets":0.2158535884657318,
48 "Nucleotide GTR":0.2090310577070883, 48 "Nucleotide GTR":0.2090998951755368,
49 "RELAX alternative":0.3058487498567987, 49 "RELAX alternative":0.3058441352816696,
50 "RELAX null":0.2559911331878715, 50 "RELAX null":0.2546949756245578,
51 "RELAX partitioned descriptive":0.3034694616209482, 51 "RELAX partitioned descriptive":0.3035514182923183,
52 "k (general descriptive)":1.926646959057857, 52 "k (general descriptive)":1.929916608813313,
53 "original name":"Horse" 53 "original name":"Horse"
54 }, 54 },
55 "Human":{ 55 "Human":{
56 "General descriptive":0, 56 "General descriptive":0,
57 "MG94xREV with separate rates for branch sets":0, 57 "MG94xREV with separate rates for branch sets":0,
58 "Nucleotide GTR":0, 58 "Nucleotide GTR":0,
59 "RELAX alternative":0, 59 "RELAX alternative":0,
60 "RELAX null":0, 60 "RELAX null":0,
61 "RELAX partitioned descriptive":0, 61 "RELAX partitioned descriptive":0,
62 "k (general descriptive)":1.462532487172471, 62 "k (general descriptive)":1.485684693044203,
63 "original name":"Human" 63 "original name":"Human"
64 }, 64 },
65 "Mouse":{ 65 "Mouse":{
66 "General descriptive":0.1307950021191255, 66 "General descriptive":0.1308809509233143,
67 "MG94xREV with separate rates for branch sets":0.1197727080219867, 67 "MG94xREV with separate rates for branch sets":0.1197584101055861,
68 "Nucleotide GTR":0.1180171198334285, 68 "Nucleotide GTR":0.1181058300538561,
69 "RELAX alternative":0.1346501492117481, 69 "RELAX alternative":0.1346294129227689,
70 "RELAX null":0.1468861666244963, 70 "RELAX null":0.1438267359449897,
71 "RELAX partitioned descriptive":0.1475623398849678, 71 "RELAX partitioned descriptive":0.148454172127534,
72 "k (general descriptive)":0.4639609139295889, 72 "k (general descriptive)":0.4625550584398252,
73 "original name":"Mouse" 73 "original name":"Mouse"
74 }, 74 },
75 "Node1":{ 75 "Node1":{
76 "General descriptive":0.350050900813081, 76 "General descriptive":0.3500691487967139,
77 "MG94xREV with separate rates for branch sets":0.2857356440257563, 77 "MG94xREV with separate rates for branch sets":0.2856782993656827,
78 "Nucleotide GTR":0.2767237570684924, 78 "Nucleotide GTR":0.2767105173979571,
79 "RELAX alternative":0.3856490868629754, 79 "RELAX alternative":0.385503346940632,
80 "RELAX null":0.4521046025119397, 80 "RELAX null":0.4352096867868785,
81 "RELAX partitioned descriptive":0.4358952685746469, 81 "RELAX partitioned descriptive":0.4379872513902164,
82 "k (general descriptive)":0.458870761901378 82 "k (general descriptive)":0.4572754180074107
83 }, 83 },
84 "Node12":{ 84 "Node12":{
85 "General descriptive":0.01766384491594095, 85 "General descriptive":0.01767932040676307,
86 "MG94xREV with separate rates for branch sets":0.01800001211221997, 86 "MG94xREV with separate rates for branch sets":0.01800350744117403,
87 "Nucleotide GTR":0.01784803874223016, 87 "Nucleotide GTR":0.01784222107494562,
88 "RELAX alternative":0.01835132674304535, 88 "RELAX alternative":0.01834159481548459,
89 "RELAX null":0.0182458522959868, 89 "RELAX null":0.01822563245625142,
90 "RELAX partitioned descriptive":0.01878351896299688, 90 "RELAX partitioned descriptive":0.01881534539472323,
91 "k (general descriptive)":0.1241597340554799 91 "k (general descriptive)":0.1240073621579099
92 }, 92 },
93 "Node2":{ 93 "Node2":{
94 "General descriptive":0.05771641706257456, 94 "General descriptive":0.05767151047612454,
95 "MG94xREV with separate rates for branch sets":0.06169547093990335, 95 "MG94xREV with separate rates for branch sets":0.06170856993599769,
96 "Nucleotide GTR":0.06613162123865737, 96 "Nucleotide GTR":0.06614755778044307,
97 "RELAX alternative":0.05450381496370671, 97 "RELAX alternative":0.0544792799094392,
98 "RELAX null":0.06144358908741494, 98 "RELAX null":0.06013052353393462,
99 "RELAX partitioned descriptive":0.05974179966710006, 99 "RELAX partitioned descriptive":0.0601550105387935,
100 "k (general descriptive)":0.5400661932123572 100 "k (general descriptive)":0.5400834620465133
101 }, 101 },
102 "Node3":{ 102 "Node3":{
103 "General descriptive":0.133048972566238, 103 "General descriptive":0.1330088052861041,
104 "MG94xREV with separate rates for branch sets":0.09736816312927643, 104 "MG94xREV with separate rates for branch sets":0.09733132151710643,
105 "Nucleotide GTR":0.09886326330774685, 105 "Nucleotide GTR":0.09883748387954429,
106 "RELAX alternative":0.1168284793254293, 106 "RELAX alternative":0.1169235247351394,
107 "RELAX null":0.1276889506286756, 107 "RELAX null":0.1263887172366205,
108 "RELAX partitioned descriptive":0.1195376339442456, 108 "RELAX partitioned descriptive":0.1196402015693241,
109 "k (general descriptive)":1.980345386854111 109 "k (general descriptive)":1.977892771876671
110 }, 110 },
111 "Node8":{ 111 "Node8":{
112 "General descriptive":0.1404364853762839, 112 "General descriptive":0.140412283431793,
113 "MG94xREV with separate rates for branch sets":0.1092041281639667, 113 "MG94xREV with separate rates for branch sets":0.1091939823455765,
114 "Nucleotide GTR":0.106239268140425, 114 "Nucleotide GTR":0.1062201244057951,
115 "RELAX alternative":0.1283918913740865, 115 "RELAX alternative":0.1284192265733904,
116 "RELAX null":0.1343238120118072, 116 "RELAX null":0.1334227466998376,
117 "RELAX partitioned descriptive":0.1363833239244288, 117 "RELAX partitioned descriptive":0.1367904558404228,
118 "k (general descriptive)":2.210166852936262 118 "k (general descriptive)":2.206967022203622
119 }, 119 },
120 "Node9":{ 120 "Node9":{
121 "General descriptive":0.02665050120918479, 121 "General descriptive":0.02664133794298214,
122 "MG94xREV with separate rates for branch sets":0.02578196090462333, 122 "MG94xREV with separate rates for branch sets":0.02578742148415842,
123 "Nucleotide GTR":0.02566573875750134, 123 "Nucleotide GTR":0.02567813733543303,
124 "RELAX alternative":0.02679622227446188, 124 "RELAX alternative":0.02680940150436639,
125 "RELAX null":0.02754241929890747, 125 "RELAX null":0.0273694783141817,
126 "RELAX partitioned descriptive":0.0274479920792393, 126 "RELAX partitioned descriptive":0.02747376898615263,
127 "k (general descriptive)":0.0733131770696667 127 "k (general descriptive)":0.07343731037788495
128 }, 128 },
129 "Pig":{ 129 "Pig":{
130 "General descriptive":0.2104601216238473, 130 "General descriptive":0.210591346560755,
131 "MG94xREV with separate rates for branch sets":0.1902977811335351, 131 "MG94xREV with separate rates for branch sets":0.1903463787974325,
132 "Nucleotide GTR":0.1871893456388788, 132 "Nucleotide GTR":0.1871390433004313,
133 "RELAX alternative":0.19752905148822, 133 "RELAX alternative":0.1974790507889271,
134 "RELAX null":0.2165309177979844, 134 "RELAX null":0.2130024973755621,
135 "RELAX partitioned descriptive":0.2074828949843082, 135 "RELAX partitioned descriptive":0.2084407457285946,
136 "k (general descriptive)":1.577441472516679, 136 "k (general descriptive)":1.581210670484469,
137 "original name":"Pig" 137 "original name":"Pig"
138 }, 138 },
139 "Rat":{ 139 "Rat":{
140 "General descriptive":0.07164210204456434, 140 "General descriptive":0.07157977734335202,
141 "MG94xREV with separate rates for branch sets":0.06709541225974219, 141 "MG94xREV with separate rates for branch sets":0.06709765698107663,
142 "Nucleotide GTR":0.06661283005976348, 142 "Nucleotide GTR":0.06661490534189227,
143 "RELAX alternative":0.07247047023746757, 143 "RELAX alternative":0.07252374836036582,
144 "RELAX null":0.07343093575256582, 144 "RELAX null":0.0734705682786943,
145 "RELAX partitioned descriptive":0.07560655472076994, 145 "RELAX partitioned descriptive":0.0757525093290258,
146 "k (general descriptive)":1.318174884032695, 146 "k (general descriptive)":1.316568267879453,
147 "original name":"Rat" 147 "original name":"Rat"
148 }, 148 },
149 "RhMonkey":{ 149 "RhMonkey":{
150 "General descriptive":0.003674505194636419, 150 "General descriptive":0.003672848089716511,
151 "MG94xREV with separate rates for branch sets":0.003716165486244973, 151 "MG94xREV with separate rates for branch sets":0.003717350789869306,
152 "Nucleotide GTR":0.003775170135617877, 152 "Nucleotide GTR":0.003778804730491441,
153 "RELAX alternative":0.003636176595806718, 153 "RELAX alternative":0.003633278464154418,
154 "RELAX null":0.003665938723426083, 154 "RELAX null":0.003661271320845124,
155 "RELAX partitioned descriptive":0.003624376345656283, 155 "RELAX partitioned descriptive":0.003625957794514879,
156 "k (general descriptive)":5.171610533872274, 156 "k (general descriptive)":5.196295069596697,
157 "original name":"RhMonkey" 157 "original name":"RhMonkey"
158 } 158 }
159 }, 159 },
160 "attributes":{ 160 "attributes":{
161 "General descriptive":{ 161 "General descriptive":{
200 "name":"relax.filter.default" 200 "name":"relax.filter.default"
201 } 201 }
202 }, 202 },
203 "fits":{ 203 "fits":{
204 "General descriptive":{ 204 "General descriptive":{
205 "AIC-c":6945.891353881681, 205 "AIC-c":6945.892677835464,
206 "Log Likelihood":-3420.486931066253, 206 "Log Likelihood":-3420.487593043145,
207 "Rate Distributions":{ 207 "Rate Distributions":{
208 "Shared":{ 208 "Shared":{
209 "0":{ 209 "0":{
210 "omega":2.202835393423959e-18, 210 "omega":2.201451464048879e-18,
211 "proportion":0.4487473029633234 211 "proportion":0.3073650505039141
212 }, 212 },
213 "1":{ 213 "1":{
214 "omega":2.202835393423959e-18, 214 "omega":2.201451464048879e-18,
215 "proportion":0.09729227592412616 215 "proportion":0.2383891488636319
216 }, 216 },
217 "2":{ 217 "2":{
218 "omega":2.202835210940273, 218 "omega":2.201451281679838,
219 "proportion":0.4539604211125504 219 "proportion":0.4542458006324541
220 } 220 }
221 } 221 }
222 }, 222 },
223 "display order":4, 223 "display order":4,
224 "estimated parameters":51 224 "estimated parameters":51
225 }, 225 },
226 "MG94xREV with separate rates for branch sets":{ 226 "MG94xREV with separate rates for branch sets":{
227 "AIC-c":6987.565999172035, 227 "AIC-c":6987.566513560764,
228 "Equilibrium frequencies": [ 228 "Equilibrium frequencies": [
229 [0.04876086397632926], 229 [0.04876086397632926],
230 [0.03982224127745371], 230 [0.03982224127745371],
231 [0.0494959405650269], 231 [0.0494959405650269],
232 [0.04152830682371345], 232 [0.04152830682371345],
286 [0.01396413011303752], 286 [0.01396413011303752],
287 [0.01140428846505027], 287 [0.01140428846505027],
288 [0.01417464125436193], 288 [0.01417464125436193],
289 [0.01189287130232129] 289 [0.01189287130232129]
290 ], 290 ],
291 "Log Likelihood":-3461.208149286616, 291 "Log Likelihood":-3461.208406480981,
292 "Rate Distributions":{ 292 "Rate Distributions":{
293 "non-synonymous/synonymous rate ratio for *Reference*": [ 293 "non-synonymous/synonymous rate ratio for *Reference*": [
294 [0.7682335289209781, 1] 294 [0.7685912547191639, 1]
295 ], 295 ],
296 "non-synonymous/synonymous rate ratio for *Test*": [ 296 "non-synonymous/synonymous rate ratio for *Test*": [
297 [1.605439824256426, 1] 297 [1.603198088111489, 1]
298 ] 298 ]
299 }, 299 },
300 "display order":1, 300 "display order":1,
301 "estimated parameters":32 301 "estimated parameters":32
302 }, 302 },
303 "Nucleotide GTR":{ 303 "Nucleotide GTR":{
304 "AIC-c":7112.857310169033, 304 "AIC-c":7112.857288723968,
305 "Equilibrium frequencies": [ 305 "Equilibrium frequencies": [
306 [0.3592490842490842], 306 [0.3592490842490842],
307 [0.181959706959707], 307 [0.181959706959707],
308 [0.240018315018315], 308 [0.240018315018315],
309 [0.2187728937728937] 309 [0.2187728937728937]
310 ], 310 ],
311 "Log Likelihood":-3532.32122446679, 311 "Log Likelihood":-3532.321213744258,
312 "Rate Distributions":{ 312 "Rate Distributions":{
313 "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087, 313 "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,
314 "Substitution rate from nucleotide A to nucleotide G":1, 314 "Substitution rate from nucleotide A to nucleotide G":1,
315 "Substitution rate from nucleotide A to nucleotide T":0.2647746107611847, 315 "Substitution rate from nucleotide A to nucleotide T":0.2646800222727828,
316 "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032, 316 "Substitution rate from nucleotide C to nucleotide G":0.4918071762416347,
317 "Substitution rate from nucleotide C to nucleotide T":1.02837595903795, 317 "Substitution rate from nucleotide C to nucleotide T":1.028675134787727,
318 "Substitution rate from nucleotide G to nucleotide T":0.304509117524575 318 "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741
319 }, 319 },
320 "display order":0, 320 "display order":0,
321 "estimated parameters":24 321 "estimated parameters":24
322 }, 322 },
323 "RELAX alternative":{ 323 "RELAX alternative":{
324 "AIC-c":6931.922980697387, 324 "AIC-c":6931.926773483473,
325 "Log Likelihood":-3429.234812770952, 325 "Log Likelihood":-3429.236709163995,
326 "Rate Distributions":{ 326 "Rate Distributions":{
327 "Reference":{ 327 "Reference":{
328 "0":{ 328 "0":{
329 "omega":1.762268314739328e-19, 329 "omega":1.761161171239182e-19,
330 "proportion":0.4504132080156107 330 "proportion":0.2691773911207853
331 }, 331 },
332 "1":{ 332 "1":{
333 "omega":1.762268314739328e-19, 333 "omega":1.762922332410267e-19,
334 "proportion":0.08749553114962015 334 "proportion":0.2692122656891806
335 }, 335 },
336 "2":{ 336 "2":{
337 "omega":2.19971015101232, 337 "omega":2.208286837998088,
338 "proportion":0.4620912608347691 338 "proportion":0.4616103431900341
339 } 339 }
340 }, 340 },
341 "Test":{ 341 "Test":{
342 "0":{ 342 "0":{
343 "omega":1.054840660215593e-44, 343 "omega":1.673670300056362e-44,
344 "proportion":0.4504132080156107 344 "proportion":0.2691773911207853
345 }, 345 },
346 "1":{ 346 "1":{
347 "omega":1.054840660215593e-44, 347 "omega":1.677579612236672e-44,
348 "proportion":0.08749553114962015 348 "proportion":0.2692122656891806
349 }, 349 },
350 "2":{ 350 "2":{
351 "omega":6.350765030542244, 351 "omega":6.354762788556926,
352 "proportion":0.4620912608347691 352 "proportion":0.4616103431900341
353 } 353 }
354 } 354 }
355 }, 355 },
356 "display order":2, 356 "display order":2,
357 "estimated parameters":36 357 "estimated parameters":36
358 }, 358 },
359 "RELAX null":{ 359 "RELAX null":{
360 "AIC-c":6946.046672507471, 360 "AIC-c":6946.648596594286,
361 "Log Likelihood":-3437.336313352972, 361 "Log Likelihood":-3437.63727539638,
362 "Rate Distributions":{ 362 "Rate Distributions":{
363 "Reference":{ 363 "Reference":{
364 "0":{ 364 "0":{
365 "omega":0.1150006822953211, 365 "omega":1.408928936991542e-20,
366 "proportion":0.542405144031307 366 "proportion":0.265244047162938
367 }, 367 },
368 "1":{ 368 "1":{
369 "omega":0.2401508033814633, 369 "omega":1.410337865928411e-20,
370 "proportion":0.08223353569636478 370 "proportion":0.28512630848952
371 }, 371 },
372 "2":{ 372 "2":{
373 "omega":3.69263720947284, 373 "omega":3.213510017765925,
374 "proportion":0.3753613202723282 374 "proportion":0.4496296443475419
375 } 375 }
376 }, 376 },
377 "Test":{ 377 "Test":{
378 "0":{ 378 "0":{
379 "omega":0.1150006822953211, 379 "omega":1.408928936991542e-20,
380 "proportion":0.542405144031307 380 "proportion":0.265244047162938
381 }, 381 },
382 "1":{ 382 "1":{
383 "omega":0.2401508033814633, 383 "omega":1.410337865928411e-20,
384 "proportion":0.08223353569636478 384 "proportion":0.28512630848952
385 }, 385 },
386 "2":{ 386 "2":{
387 "omega":3.69263720947284, 387 "omega":3.213510017765925,
388 "proportion":0.3753613202723282 388 "proportion":0.4496296443475419
389 } 389 }
390 } 390 }
391 }, 391 },
392 "display order":3, 392 "display order":3,
393 "estimated parameters":35 393 "estimated parameters":35
394 }, 394 },
395 "RELAX partitioned descriptive":{ 395 "RELAX partitioned descriptive":{
396 "AIC-c":6937.04707353565, 396 "AIC-c":6937.049237937651,
397 "Log Likelihood":-3427.626871923648, 397 "Log Likelihood":-3427.627954124649,
398 "Rate Distributions":{ 398 "Rate Distributions":{
399 "Reference":{ 399 "Reference":{
400 "0":{ 400 "0":{
401 "omega":0.1943306885168281, 401 "omega":0.1847557016619168,
402 "proportion":0.3359458135547653 402 "proportion":0.4766160247339328
403 }, 403 },
404 "1":{ 404 "1":{
405 "omega":0.2607558478587815, 405 "omega":0.3367540359539261,
406 "proportion":0.4332550437039296 406 "proportion":0.3005513276312735
407 }, 407 },
408 "2":{ 408 "2":{
409 "omega":4.134271224300374, 409 "omega":4.272816072857538,
410 "proportion":0.2307991427413052 410 "proportion":0.2228326476347937
411 } 411 }
412 }, 412 },
413 "Test":{ 413 "Test":{
414 "0":{ 414 "0":{
415 "omega":0, 415 "omega":1.127143149593234e-21,
416 "proportion":0.4753488415962343 416 "proportion":0.2367540589657237
417 }, 417 },
418 "1":{ 418 "1":{
419 "omega":0, 419 "omega":1.128270292740756e-21,
420 "proportion":0.03858318603767072 420 "proportion":0.2771164325302933
421 }, 421 },
422 "2":{ 422 "2":{
423 "omega":6.017221959238516, 423 "omega":6.023626417874829,
424 "proportion":0.486067972366095 424 "proportion":0.4861295085039831
425 } 425 }
426 } 426 }
427 }, 427 },
428 "display order":5, 428 "display order":5,
429 "estimated parameters":40 429 "estimated parameters":40
430 } 430 }
431 }, 431 },
432 "input":{ 432 "input":{
433 "file name":"/tmp/tmpbauyxvdv/job_working_directory/000/3/working/./input.fasta", 433 "file name":"/tmp/tmpkgsdjj1d/job_working_directory/000/3/working/./input.fasta",
434 "number of sequences":10, 434 "number of sequences":10,
435 "number of sites":187, 435 "number of sites":187,
436 "partition count":1, 436 "partition count":1,
437 "trees":{ 437 "trees":{
438 "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)" 438 "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)"
439 } 439 }
440 }, 440 },
441 "runtime":"2.5.32",
441 "test results":{ 442 "test results":{
442 "LRT":16.20300116404087, 443 "LRT":16.80113246476958,
443 "p-value":5.690389451429301e-05, 444 "p-value":4.150852429507523e-05,
444 "relaxation or intensification parameter":2.344938789085876 445 "relaxation or intensification parameter":2.334214628944839
445 }, 446 },
446 "tested":{ 447 "tested":{
447 "0":{ 448 "0":{
448 "Baboon":"Reference", 449 "Baboon":"Reference",
449 "Cat":"Test", 450 "Cat":"Test",
464 } 465 }
465 }, 466 },
466 "timers":{ 467 "timers":{
467 "General descriptive model fitting":{ 468 "General descriptive model fitting":{
468 "order":2, 469 "order":2,
469 "timer":132 470 "timer":127
470 }, 471 },
471 "Overall":{ 472 "Overall":{
472 "order":0, 473 "order":0,
473 "timer":324 474 "timer":396
474 }, 475 },
475 "Preliminary model fitting":{ 476 "Preliminary model fitting":{
476 "order":1, 477 "order":1,
477 "timer":8 478 "timer":8
478 }, 479 },
479 "RELAX alternative model fitting":{ 480 "RELAX alternative model fitting":{
480 "order":3, 481 "order":3,
481 "timer":65 482 "timer":103
482 }, 483 },
483 "RELAX null model fitting":{ 484 "RELAX null model fitting":{
484 "order":4, 485 "order":4,
485 "timer":66 486 "timer":41
486 }, 487 },
487 "RELAX partitioned descriptive":{ 488 "RELAX partitioned descriptive":{
488 "order":5, 489 "order":5,
489 "timer":53 490 "timer":116
490 } 491 }
491 } 492 }
492 } 493 }