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comparison test-data/absrel-out1.json @ 15:91006eb8b84e 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 21:10:23 +0000
parents bf97cacc1a55
children
comparison
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14:a54340ea0866 15:91006eb8b84e
1 { 1 {
2 "analysis":{ 2 "analysis":{
3 "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
4 "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",
5 "contact":"spond@temple.edu",
3 "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.", 6 "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.",
4 "version":"2.0", 7 "requirements":"in-frame codon alignment and a phylogenetic tree",
5 "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", 8 "version":"2.2"
6 "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group", 9 },
7 "contact":"spond@temple.edu", 10 "branch attributes":{
8 "requirements":"in-frame codon alignment and a phylogenetic tree" 11 "0":{
12 "Baboon":{
13 "Baseline MG94xREV":0.001816807585564731,
14 "Baseline MG94xREV omega ratio":0,
15 "Corrected P-value":1,
16 "Full adaptive model":0.001810407118394509,
17 "LRT":0,
18 "Nucleotide GTR":0.001678881906620672,
19 "Rate Distributions": [
20 [0, 1]
21 ],
22 "Rate classes":1,
23 "Uncorrected P-value":1,
24 "original name":"Baboon",
25 "rate at which 2 nucleotides are changed instantly within a single codon":0
26 },
27 "Cat":{
28 "Baseline MG94xREV":0.2286001363527903,
29 "Baseline MG94xREV omega ratio":1.403298474422089,
30 "Corrected P-value":1,
31 "Full adaptive model":0.1219386838393392,
32 "LRT":1.644967676056694,
33 "Nucleotide GTR":0.265904547400163,
34 "Rate Distributions": [
35 [0.2130519766306851, 0.6352283641519592],
36 [2.628217450705319, 0.3647716358480408]
37 ],
38 "Rate classes":2,
39 "Uncorrected P-value":0.171730764045231,
40 "original name":"Cat",
41 "rate at which 2 nucleotides are changed instantly within a single codon":0
42 },
43 "Chimp":{
44 "Baseline MG94xREV":0.001840311209746262,
45 "Baseline MG94xREV omega ratio":10000000000,
46 "Corrected P-value":1,
47 "Full adaptive model":0.001841979303044237,
48 "LRT":0.6159123786974305,
49 "Nucleotide GTR":0.001816713800925801,
50 "Rate Distributions": [
51 [10000000000, 1]
52 ],
53 "Rate classes":1,
54 "Uncorrected P-value":0.3069983227523322,
55 "original name":"Chimp",
56 "rate at which 2 nucleotides are changed instantly within a single codon":0
57 },
58 "Cow":{
59 "Baseline MG94xREV":0.2070244948790512,
60 "Baseline MG94xREV omega ratio":2.153434974462683,
61 "Corrected P-value":0.5006146299996015,
62 "Full adaptive model":0.1241125417707662,
63 "LRT":4.898194538953248,
64 "Nucleotide GTR":0.2481512612523618,
65 "Rate Distributions": [
66 [0, 0.52318726440949],
67 [2.444056517734385, 0.47681273559051]
68 ],
69 "Rate classes":2,
70 "Uncorrected P-value":0.03128841437497509,
71 "original name":"Cow",
72 "rate at which 2 nucleotides are changed instantly within a single codon":0
73 },
74 "Horse":{
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78 "Full adaptive model":0.0869489794025302,
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80 "Nucleotide GTR":0.2090927256979082,
81 "Rate Distributions": [
82 [0, 0.5397658078247131],
83 [1.633257246666139, 0.4602341921752869]
84 ],
85 "Rate classes":2,
86 "Uncorrected P-value":0.1382789032066179,
87 "original name":"Horse",
88 "rate at which 2 nucleotides are changed instantly within a single codon":0
89 },
90 "Human":{
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92 "Baseline MG94xREV omega ratio":1,
93 "Corrected P-value":1,
94 "Full adaptive model":0,
95 "LRT":0,
96 "Nucleotide GTR":0,
97 "Rate Distributions": [
98 [1, 1]
99 ],
100 "Rate classes":1,
101 "Uncorrected P-value":1,
102 "original name":"Human",
103 "rate at which 2 nucleotides are changed instantly within a single codon":0.0006106118725184574
104 },
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108 "Corrected P-value":1,
109 "Full adaptive model":0.1078010043714489,
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111 "Nucleotide GTR":0.1181001275359051,
112 "Rate Distributions": [
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114 ],
115 "Rate classes":1,
116 "Uncorrected P-value":1,
117 "original name":"Mouse",
118 "rate at which 2 nucleotides are changed instantly within a single codon":0.4244832903005548
119 },
120 "Node1":{
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122 "Baseline MG94xREV omega ratio":0.2997498382776075,
123 "Corrected P-value":1,
124 "Full adaptive model":0.2550466752020236,
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126 "Nucleotide GTR":0.2767426965701868,
127 "Rate Distributions": [
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129 ],
130 "Rate classes":1,
131 "Uncorrected P-value":1,
132 "rate at which 2 nucleotides are changed instantly within a single codon":0.9114373463003921
133 },
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137 "Corrected P-value":1,
138 "Full adaptive model":0.01437973904273591,
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140 "Nucleotide GTR":0.01784721909304638,
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143 ],
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147 },
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160 "rate at which 2 nucleotides are changed instantly within a single codon":9.28646275825122
161 },
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166 "Full adaptive model":0.08590119038008139,
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168 "Nucleotide GTR":0.09881178513658169,
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174 "rate at which 2 nucleotides are changed instantly within a single codon":0.8390789546113498
175 },
176 "Node8":{
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179 "Corrected P-value":1,
180 "Full adaptive model":0.0958035263641453,
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182 "Nucleotide GTR":0.1062333225692588,
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185 ],
186 "Rate classes":1,
187 "Uncorrected P-value":0.2893795680778183,
188 "rate at which 2 nucleotides are changed instantly within a single codon":0.512238843416092
189 },
190 "Node9":{
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192 "Baseline MG94xREV omega ratio":0.4321055128385307,
193 "Corrected P-value":1,
194 "Full adaptive model":0.02810856974543091,
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196 "Nucleotide GTR":0.02566185438854229,
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199 ],
200 "Rate classes":1,
201 "Uncorrected P-value":1,
202 "rate at which 2 nucleotides are changed instantly within a single codon":0
203 },
204 "Pig":{
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208 "Full adaptive model":0.1729188354138871,
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210 "Nucleotide GTR":0.1871760137183495,
211 "Rate Distributions": [
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213 ],
214 "Rate classes":1,
215 "Uncorrected P-value":0.3669120164240152,
216 "original name":"Pig",
217 "rate at which 2 nucleotides are changed instantly within a single codon":0.1143447431158695
218 },
219 "Rat":{
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223 "Full adaptive model":0.06408078523886611,
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225 "Nucleotide GTR":0.0666364425850592,
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228 ],
229 "Rate classes":1,
230 "Uncorrected P-value":1,
231 "original name":"Rat",
232 "rate at which 2 nucleotides are changed instantly within a single codon":0.1346164190615118
233 },
234 "RhMonkey":{
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237 "Corrected P-value":1,
238 "Full adaptive model":0.003675047654636179,
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240 "Nucleotide GTR":0.003777016173741061,
241 "Rate Distributions": [
242 [10000000000, 1]
243 ],
244 "Rate classes":1,
245 "Uncorrected P-value":0.2236284592802686,
246 "original name":"RhMonkey",
247 "rate at which 2 nucleotides are changed instantly within a single codon":0
248 }
249 },
250 "attributes":{
251 "Baseline MG94xREV":{
252 "attribute type":"branch length",
253 "display order":1
254 },
255 "Baseline MG94xREV omega ratio":{
256 "attribute type":"branch label",
257 "display order":1
258 },
259 "Corrected P-value":{
260 "attribute type":"branch label",
261 "display order":6
262 },
263 "Full adaptive model":{
264 "attribute type":"branch length",
265 "display order":2
266 },
267 "LRT":{
268 "attribute type":"branch label",
269 "display order":4
270 },
271 "Nucleotide GTR":{
272 "attribute type":"branch length",
273 "display order":0
274 },
275 "Rate Distributions":{
276 "attribute type":"branch label",
277 "display order":3
278 },
279 "Rate classes":{
280 "attribute type":"branch label",
281 "display order":2
282 },
283 "Uncorrected P-value":{
284 "attribute type":"branch label",
285 "display order":5
286 },
287 "original name":{
288 "attribute type":"node label",
289 "display order":-1
290 },
291 "rate at which 2 nucleotides are changed instantly within a single codon":{
292 "attribute type":"branch label",
293 "display order":7
294 }
295 }
296 },
297 "data partitions":{
298 "0":{
299 "coverage": [
300 [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]
301 ],
302 "name":"absrel.filter.default"
303 }
304 },
305 "fits":{
306 "Baseline MG94xREV":{
307 "AIC-c":6983.763305606333,
308 "Equilibrium frequencies": [
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310 [0.03982858547830345],
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363 [0.007626222986467745],
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366 [0.01395367801862353],
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368 [0.01415821524731906],
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370 ],
371 "Log Likelihood":-3427.720059001285,
372 "Rate Distributions":{
373 "Per-branch delta":{
374 "2.5%":0,
375 "97.5%":12.07373117808175,
376 "Mean":1.277646334033236,
377 "Median":0.4551223038316586
378 },
379 "Per-branch omega":{
380 "2.5%":0,
381 "97.5%":2.153434974462683,
382 "Mean":666666667.5119981,
383 "Median":1
384 }
385 },
386 "display order":1,
387 "estimated parameters":62
388 },
389 "Full adaptive model":{
390 "AIC-c":6972.859938351839,
391 "Log Likelihood":-3415.824749853321,
392 "Rate Distributions":{
393 },
394 "display order":2,
395 "estimated parameters":68
396 },
397 "Nucleotide GTR":{
398 "AIC-c":7112.857317645923,
399 "Equilibrium frequencies": [
400 [0.3592490842490842],
401 [0.181959706959707],
402 [0.240018315018315],
403 [0.2187728937728937]
404 ],
405 "Log Likelihood":-3532.321228205235,
406 "Rate Distributions":{
407 "Substitution rate from nucleotide A to nucleotide C":0.5498703043473002,
408 "Substitution rate from nucleotide A to nucleotide G":1,
409 "Substitution rate from nucleotide A to nucleotide T":0.2646979624678532,
410 "Substitution rate from nucleotide C to nucleotide G":0.4921328068285813,
411 "Substitution rate from nucleotide C to nucleotide T":1.028960084526602,
412 "Substitution rate from nucleotide G to nucleotide T":0.3044365000595399
413 },
414 "display order":0,
415 "estimated parameters":24
416 }
9 }, 417 },
10 "input":{ 418 "input":{
11 "file name":"/tmp/tmpCAMqUO/job_working_directory/002/2602/working/absrel_input.fa", 419 "file name":"/tmp/tmpx_42i6f0/job_working_directory/000/6/working/./absrel_input.fa",
12 "number of sequences":10, 420 "number of sequences":10,
13 "number of sites":187, 421 "number of sites":187,
14 "partition count":1, 422 "partition count":1,
15 "trees":{ 423 "trees":{
16 "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)" 424 "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)"
17 }
18 },
19 "fits":{
20 "Nucleotide GTR":{
21 "Log Likelihood":-3531.96369518556,
22 "estimated parameters":24,
23 "AIC-c":7112.577796875186,
24 "Equilibrium frequencies":[
25 [0.3563279857397504],
26 [0.1837789661319073],
27 [0.2402852049910873],
28 [0.2196078431372549]
29 ],
30 "Rate Distributions":{
31 "Substitution rate from nucleotide A to nucleotide C":0.5474707834424497,
32 "Substitution rate from nucleotide A to nucleotide G":1,
33 "Substitution rate from nucleotide A to nucleotide T":0.2645731370379643,
34 "Substitution rate from nucleotide C to nucleotide G":0.4867482826410435,
35 "Substitution rate from nucleotide C to nucleotide T":1.018295973581558,
36 "Substitution rate from nucleotide G to nucleotide T":0.3026112531229544
37 },
38 "display order":0
39 },
40 "Baseline MG94xREV":{
41 "Log Likelihood":-3450.669934819203,
42 "estimated parameters":46,
43 "AIC-c":6995.711784065174,
44 "Equilibrium frequencies":[
45 [0.04787662253946073],
46 [0.03913388100305117],
47 [0.04844580322128512],
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101 [0.008174012048031599],
102 [0.01413784690564137],
103 [0.01155613719386138],
104 [0.01430592453757226],
105 [0.01202389319448819]
106 ],
107 "Rate Distributions":{
108 "Per-branch omega":{
109 "Mean":666666667.6064719,
110 "Median":1.103169534345197,
111 "2.5%":0,
112 "97.5%":10000000000
113 }
114 },
115 "display order":1
116 },
117 "Full adaptive model":{
118 "Log Likelihood":-3414.992415597899,
119 "estimated parameters":60,
120 "AIC-c":6954.031265689993,
121 "Rate Distributions":{
122 },
123 "display order":2
124 }
125 },
126 "timers":{
127 "Overall":{
128 "timer":98,
129 "order":0
130 },
131 "Preliminary model fitting":{
132 "timer":0,
133 "order":1
134 },
135 "Baseline model fitting":{
136 "timer":1,
137 "order":2
138 },
139 "Complexity analysis":{
140 "timer":36,
141 "order":3
142 },
143 "Full adaptive model fitting":{
144 "timer":8,
145 "order":4
146 },
147 "Testing for selection":{
148 "timer":53,
149 "order":5
150 } 425 }
151 }, 426 },
152 "test results":{ 427 "test results":{
153 "P-value threshold":0.05, 428 "P-value threshold":0.05,
154 "tested":16, 429 "positive test results":0,
155 "positive test results":3 430 "tested":16
156 }, 431 },
157 "tested":{ 432 "tested":{
158 "0":{ 433 "0":{
434 "Baboon":"test",
435 "Cat":"test",
436 "Chimp":"test",
437 "Cow":"test",
438 "Horse":"test",
439 "Human":"test",
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456 } 478 }