comparison test-data/absrel-out1.json @ 16:47145f568cd6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"
author iuc
date Fri, 18 Sep 2020 21:11:31 +0000
parents fe399429a5d2
children
comparison
equal deleted inserted replaced
15:600647840e87 16:47145f568cd6
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":{
75 "Baseline MG94xREV":0.190365915457708,
76 "Baseline MG94xREV omega ratio":1.182933895494305,
77 "Corrected P-value":1,
78 "Full adaptive model":0.0869489794025302,
79 "LRT":2.047309801283518,
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":{
91 "Baseline MG94xREV":0,
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 },
105 "Mouse":{
106 "Baseline MG94xREV":0.1083167307250788,
107 "Baseline MG94xREV omega ratio":0.5108576904540283,
108 "Corrected P-value":1,
109 "Full adaptive model":0.1078010043714489,
110 "LRT":0,
111 "Nucleotide GTR":0.1181001275359051,
112 "Rate Distributions": [
113 [0.5087375113796073, 1]
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":{
121 "Baseline MG94xREV":0.2542393300501047,
122 "Baseline MG94xREV omega ratio":0.2997498382776075,
123 "Corrected P-value":1,
124 "Full adaptive model":0.2550466752020236,
125 "LRT":0,
126 "Nucleotide GTR":0.2767426965701868,
127 "Rate Distributions": [
128 [0.2932817609633239, 1]
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 },
134 "Node12":{
135 "Baseline MG94xREV":0.01400815185374474,
136 "Baseline MG94xREV omega ratio":0.2754467062829232,
137 "Corrected P-value":1,
138 "Full adaptive model":0.01437973904273591,
139 "LRT":0,
140 "Nucleotide GTR":0.01784721909304638,
141 "Rate Distributions": [
142 [0.3037614070859027, 1]
143 ],
144 "Rate classes":1,
145 "Uncorrected P-value":1,
146 "rate at which 2 nucleotides are changed instantly within a single codon":0.5084909616267814
147 },
148 "Node2":{
149 "Baseline MG94xREV":0.0400106272595141,
150 "Baseline MG94xREV omega ratio":0.116408812566168,
151 "Corrected P-value":1,
152 "Full adaptive model":0.03991940069030483,
153 "LRT":0,
154 "Nucleotide GTR":0.06613304839358287,
155 "Rate Distributions": [
156 [0.1193993042178124, 1]
157 ],
158 "Rate classes":1,
159 "Uncorrected P-value":1,
160 "rate at which 2 nucleotides are changed instantly within a single codon":9.28646275825122
161 },
162 "Node3":{
163 "Baseline MG94xREV":0.08548068002443369,
164 "Baseline MG94xREV omega ratio":1.293385437932658,
165 "Corrected P-value":1,
166 "Full adaptive model":0.08590119038008139,
167 "LRT":0.1383887036890883,
168 "Nucleotide GTR":0.09881178513658169,
169 "Rate Distributions": [
170 [1.330576641567385, 1]
171 ],
172 "Rate classes":1,
173 "Uncorrected P-value":0.4219212196398351,
174 "rate at which 2 nucleotides are changed instantly within a single codon":0.8390789546113498
175 },
176 "Node8":{
177 "Baseline MG94xREV":0.09463393920061362,
178 "Baseline MG94xREV omega ratio":1.862136443854597,
179 "Corrected P-value":1,
180 "Full adaptive model":0.0958035263641453,
181 "LRT":0.7150293976401372,
182 "Nucleotide GTR":0.1062333225692588,
183 "Rate Distributions": [
184 [1.883870769808856, 1]
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":{
191 "Baseline MG94xREV":0.02846111726225027,
192 "Baseline MG94xREV omega ratio":0.4321055128385307,
193 "Corrected P-value":1,
194 "Full adaptive model":0.02810856974543091,
195 "LRT":0,
196 "Nucleotide GTR":0.02566185438854229,
197 "Rate Distributions": [
198 [0.4185836885800617, 1]
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":{
205 "Baseline MG94xREV":0.1782835053555321,
206 "Baseline MG94xREV omega ratio":1.275728452678247,
207 "Corrected P-value":1,
208 "Full adaptive model":0.1729188354138871,
209 "LRT":0.3324036585026988,
210 "Nucleotide GTR":0.1871760137183495,
211 "Rate Distributions": [
212 [1.235108129487059, 1]
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":{
220 "Baseline MG94xREV":0.06315403896300904,
221 "Baseline MG94xREV omega ratio":0.8744850915248316,
222 "Corrected P-value":1,
223 "Full adaptive model":0.06408078523886611,
224 "LRT":0,
225 "Nucleotide GTR":0.0666364425850592,
226 "Rate Distributions": [
227 [0.8782045320352186, 1]
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":{
235 "Baseline MG94xREV":0.003671939837747083,
236 "Baseline MG94xREV omega ratio":10000000000,
237 "Corrected P-value":1,
238 "Full adaptive model":0.003675047654636179,
239 "LRT":1.165062770327495,
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": [
309 [0.04875339327772683],
310 [0.03982858547830345],
311 [0.04946803524790992],
312 [0.04152216138298744],
313 [0.01811683453600613],
314 [0.01480036248560469],
315 [0.0183823965708893],
316 [0.01542969784826435],
317 [0.01894694796506697],
318 [0.01547851515238824],
319 [0.01922467805342367],
320 [0.01613668666381816],
321 [0.02832099415740372],
322 [0.02313654621336914],
323 [0.02873613184734657],
324 [0.02412034959764736],
325 [0.01662182431200483],
326 [0.01357902918971745],
327 [0.01686547203528639],
328 [0.01415643148428886],
329 [0.006176695005242439],
330 [0.005045987744654046],
331 [0.006267234867003878],
332 [0.005260551308914496],
333 [0.006459711194459957],
334 [0.005277194922783805],
335 [0.006554399593040238],
336 [0.005501589790395056],
337 [0.009655668202293983],
338 [0.007888099278638223],
339 [0.009797203904398108],
340 [0.008223514024394991],
341 [0.03326722643528176],
342 [0.02717732003095303],
343 [0.03375486749252685],
344 [0.02833294365668738],
345 [0.01236215156074466],
346 [0.01009913314808799],
347 [0.01254335971371867],
348 [0.01052856463184265],
349 [0.01292858539344675],
350 [0.0105618754683007],
351 [0.0131180965046964],
352 [0.01101098350431497],
353 [0.0193250328267319],
354 [0.01578738770911659],
355 [0.0196083049972345],
356 [0.01645869298147252],
357 [0.01962343746171723],
358 [0.02045785777700414],
359 [0.008926115885166477],
360 [0.007292098982657142],
361 [0.009056957588961733],
362 [0.007602170831388156],
363 [0.007626222986467745],
364 [0.009471947420992787],
365 [0.007950502328516303],
366 [0.01395367801862353],
367 [0.01139931439306339],
368 [0.01415821524731906],
369 [0.01188403168729233]
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],
48 [0.0407178971288476],
49 [0.01817959331488358],
50 [0.01485982100934833],
51 [0.01839572120297191],
52 [0.01546129971531724],
53 [0.0190238172858878],
54 [0.01554988139098808],
55 [0.01924998172104109],
56 [0.01617929156565557],
57 [0.02798385246472159],
58 [0.02287372613761008],
59 [0.02831653817605838],
60 [0.02379958245776909],
61 [0.01680670574479072],
62 [0.01373763619452979],
63 [0.01700651207463693],
64 [0.01429369239710176],
65 [0.006381800954137531],
66 [0.005216421415661322],
67 [0.006457670922102578],
68 [0.00542756570877943],
69 [0.006678159032689796],
70 [0.005458661598138652],
71 [0.00675755225029668],
72 [0.00567961101013393],
73 [0.009823507779659469],
74 [0.008029638769211124],
75 [0.009940294440024354],
76 [0.008354653231583485],
77 [0.0329096029621651],
78 [0.02689998621179963],
79 [0.03330084840219455],
80 [0.02798881284619018],
81 [0.01249635346589736],
82 [0.01021439657952951],
83 [0.01264491622176376],
84 [0.01062784315018763],
85 [0.01307665913959002],
86 [0.01068873273724336],
87 [0.0132321208528494],
88 [0.01112137894012831],
89 [0.01923563996618058],
90 [0.01572302316926395],
91 [0.01946432265285621],
92 [0.01635944157725275],
93 [0.01977100255021048],
94 [0.02057127040149398],
95 [0.009184593415672956],
96 [0.007507396443725858],
97 [0.009293784349897772],
98 [0.007811272183233558],
99 [0.007856024926654371],
100 [0.009725369116048951],
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",
440 "Mouse":"test",
441 "Node1":"test",
442 "Node12":"test",
443 "Node2":"test",
444 "Node3":"test",
445 "Node8":"test",
446 "Node9":"test",
159 "Pig":"test", 447 "Pig":"test",
160 "Cow":"test",
161 "Node3":"test",
162 "Horse":"test",
163 "Cat":"test",
164 "Node2":"test",
165 "RhMonkey":"test",
166 "Baboon":"test",
167 "Node9":"test",
168 "Human":"test",
169 "Chimp":"test",
170 "Node12":"test",
171 "Node8":"test",
172 "Node1":"test",
173 "Rat":"test", 448 "Rat":"test",
174 "Mouse":"test" 449 "RhMonkey":"test"
175 } 450 }
176 }, 451 },
177 "data partitions":{ 452 "timers":{
178 "0":{ 453 "Baseline model fitting":{
179 "name":"absrel.filter.default", 454 "order":2,
180 "coverage":[ 455 "timer":17
181 [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] 456 },
182 ] 457 "Complexity analysis":{
183 } 458 "order":3,
184 }, 459 "timer":110
185 "branch attributes":{ 460 },
186 "0":{ 461 "Full adaptive model fitting":{
187 "Human":{ 462 "order":4,
188 "original name":"Human", 463 "timer":20
189 "Nucleotide GTR":0, 464 },
190 "Baseline MG94xREV":0, 465 "Overall":{
191 "Baseline MG94xREV omega ratio":1, 466 "order":0,
192 "Rate classes":1, 467 "timer":259
193 "Full adaptive model":0, 468 },
194 "Rate Distributions":[ 469 "Preliminary model fitting":{
195 [1, 1] 470 "order":1,
196 ], 471 "timer":0
197 "LRT":0, 472 },
198 "Uncorrected P-value":1, 473 "Testing for selection":{
199 "Corrected P-value":1 474 "order":5,
200 }, 475 "timer":112
201 "Chimp":{
202 "original name":"Chimp",
203 "Nucleotide GTR":0.001818174796225333,
204 "Baseline MG94xREV":0.001839770270131542,
205 "Baseline MG94xREV omega ratio":10000000000,
206 "Rate classes":1,
207 "Full adaptive model":0.001845806111200226,
208 "Rate Distributions":[
209 [10000000000, 1]
210 ],
211 "LRT":0.6362875427803374,
212 "Uncorrected P-value":0.303261123771571,
213 "Corrected P-value":1
214 },
215 "Baboon":{
216 "original name":"Baboon",
217 "Nucleotide GTR":0.001682034724848474,
218 "Baseline MG94xREV":0.001821072110941238,
219 "Baseline MG94xREV omega ratio":0,
220 "Rate classes":1,
221 "Full adaptive model":0.001808294153407354,
222 "Rate Distributions":[
223 [0, 1]
224 ],
225 "LRT":0,
226 "Uncorrected P-value":1,
227 "Corrected P-value":1
228 },
229 "RhMonkey":{
230 "original name":"RhMonkey",
231 "Nucleotide GTR":0.003775509884015639,
232 "Baseline MG94xREV":0.003671340584166445,
233 "Baseline MG94xREV omega ratio":10000000000,
234 "Rate classes":1,
235 "Full adaptive model":0.003682180830540259,
236 "Rate Distributions":[
237 [10000000000, 1]
238 ],
239 "LRT":1.200615147074132,
240 "Uncorrected P-value":0.2192326116145807,
241 "Corrected P-value":1
242 },
243 "Cow":{
244 "original name":"Cow",
245 "Nucleotide GTR":0.248257545271419,
246 "Baseline MG94xREV":0.2535517510207829,
247 "Baseline MG94xREV omega ratio":1.957039676836281,
248 "Rate classes":2,
249 "Full adaptive model":0.3959632497370367,
250 "Rate Distributions":[
251 [0, 0.5384412409742189],
252 [10.58123012791267, 0.4615587590257811]
253 ],
254 "LRT":24.50128746473001,
255 "Uncorrected P-value":1.583131814197891e-06,
256 "Corrected P-value":2.533010902716626e-05
257 },
258 "Pig":{
259 "original name":"Pig",
260 "Nucleotide GTR":0.1872143003439852,
261 "Baseline MG94xREV":0.1913752025483544,
262 "Baseline MG94xREV omega ratio":1.354835319497051,
263 "Rate classes":1,
264 "Full adaptive model":0.1823079562415392,
265 "Rate Distributions":[
266 [1.270031670375847, 1]
267 ],
268 "LRT":0.5083013304356427,
269 "Uncorrected P-value":0.3278475069550038,
270 "Corrected P-value":1
271 },
272 "Horse":{
273 "original name":"Horse",
274 "Nucleotide GTR":0.2092211101976542,
275 "Baseline MG94xREV":0.2093433205074538,
276 "Baseline MG94xREV omega ratio":1.262933703792719,
277 "Rate classes":2,
278 "Full adaptive model":0.2696870893488891,
279 "Rate Distributions":[
280 [0, 0.5494326491453121],
281 [4.447670371762946, 0.4505673508546879]
282 ],
283 "LRT":9.839972152766677,
284 "Uncorrected P-value":0.002531289908698275,
285 "Corrected P-value":0.03543805872177586
286 },
287 "Cat":{
288 "original name":"Cat",
289 "Nucleotide GTR":0.2662269345134692,
290 "Baseline MG94xREV":0.2773733494290757,
291 "Baseline MG94xREV omega ratio":1.619113019542315,
292 "Rate classes":2,
293 "Full adaptive model":0.3637840333790108,
294 "Rate Distributions":[
295 [0.3427137549260186, 0.5775012741005606],
296 [6.025097508634321, 0.4224987258994394]
297 ],
298 "LRT":13.05292728184577,
299 "Uncorrected P-value":0.000499814517576469,
300 "Corrected P-value":0.007497217763647035
301 },
302 "Mouse":{
303 "original name":"Mouse",
304 "Nucleotide GTR":0.1181551390736968,
305 "Baseline MG94xREV":0.1220127721537473,
306 "Baseline MG94xREV omega ratio":0.5307054960008202,
307 "Rate classes":1,
308 "Full adaptive model":0.1200052061883895,
309 "Rate Distributions":[
310 [0.5418818043457002, 1]
311 ],
312 "LRT":0,
313 "Uncorrected P-value":1,
314 "Corrected P-value":1
315 },
316 "Rat":{
317 "original name":"Rat",
318 "Nucleotide GTR":0.06673994656462794,
319 "Baseline MG94xREV":0.06546903135094065,
320 "Baseline MG94xREV omega ratio":1.103169534345197,
321 "Rate classes":1,
322 "Full adaptive model":0.06894368446818594,
323 "Rate Distributions":[
324 [1.162844601638596, 1]
325 ],
326 "LRT":0.04180897168953379,
327 "Uncorrected P-value":0.4613906175252571,
328 "Corrected P-value":1
329 },
330 "Node1":{
331 "Nucleotide GTR":0.2772613398768408,
332 "Baseline MG94xREV":0.2903229694372956,
333 "Baseline MG94xREV omega ratio":0.4389914526526448,
334 "Rate classes":2,
335 "Full adaptive model":0.3664538683295676,
336 "Rate Distributions":[
337 [0.1934444279004118, 0.7920338324503209],
338 [2.595458156723663, 0.2079661675496791]
339 ],
340 "LRT":1.095302853601424,
341 "Uncorrected P-value":0.232551772988317,
342 "Corrected P-value":1
343 },
344 "Node12":{
345 "Nucleotide GTR":0.01783922546179193,
346 "Baseline MG94xREV":0.01797212760838867,
347 "Baseline MG94xREV omega ratio":0.3712490894908597,
348 "Rate classes":1,
349 "Full adaptive model":0.01648897148329989,
350 "Rate Distributions":[
351 [0.3341484726344874, 1]
352 ],
353 "LRT":0,
354 "Uncorrected P-value":1,
355 "Corrected P-value":1
356 },
357 "Node2":{
358 "Nucleotide GTR":0.06619058539001231,
359 "Baseline MG94xREV":0.06580724801157116,
360 "Baseline MG94xREV omega ratio":0.6811307469311604,
361 "Rate classes":2,
362 "Full adaptive model":0.1259563484776556,
363 "Rate Distributions":[
364 [0, 0.902872882268449],
365 [33.80023214939837, 0.09712711773155103]
366 ],
367 "LRT":7.670975764417562,
368 "Uncorrected P-value":0.007599562698001494,
369 "Corrected P-value":0.09119475237601793
370 },
371 "Node3":{
372 "Nucleotide GTR":0.09883236156840018,
373 "Baseline MG94xREV":0.102749851157051,
374 "Baseline MG94xREV omega ratio":1.47449378631578,
375 "Rate classes":2,
376 "Full adaptive model":0.1389308407753113,
377 "Rate Distributions":[
378 [0, 0.7024206790833775],
379 [8.065310624699681, 0.2975793209166225]
380 ],
381 "LRT":6.598417720076213,
382 "Uncorrected P-value":0.0131150962965953,
383 "Corrected P-value":0.1442660592625483
384 },
385 "Node8":{
386 "Nucleotide GTR":0.1061134663636472,
387 "Baseline MG94xREV":0.110140333084973,
388 "Baseline MG94xREV omega ratio":1.896243438714738,
389 "Rate classes":2,
390 "Full adaptive model":0.2165540926910564,
391 "Rate Distributions":[
392 [1, 0.9077840705139004],
393 [33.32075865076668, 0.09221592948609958]
394 ],
395 "LRT":7.97288393366216,
396 "Uncorrected P-value":0.006519360772582139,
397 "Corrected P-value":0.08475169004356781
398 },
399 "Node9":{
400 "Nucleotide GTR":0.02566719422260768,
401 "Baseline MG94xREV":0.02590165433349057,
402 "Baseline MG94xREV omega ratio":0.4071738826525522,
403 "Rate classes":1,
404 "Full adaptive model":0.02766629863085238,
405 "Rate Distributions":[
406 [0.4488424899910019, 1]
407 ],
408 "LRT":0,
409 "Uncorrected P-value":1,
410 "Corrected P-value":1
411 }
412 },
413 "attributes":{
414 "original name":{
415 "attribute type":"node label",
416 "display order":-1
417 },
418 "Nucleotide GTR":{
419 "attribute type":"branch length",
420 "display order":0
421 },
422 "Baseline MG94xREV":{
423 "attribute type":"branch length",
424 "display order":1
425 },
426 "Baseline MG94xREV omega ratio":{
427 "attribute type":"branch label",
428 "display order":1
429 },
430 "Rate classes":{
431 "attribute type":"branch label",
432 "display order":2
433 },
434 "Full adaptive model":{
435 "attribute type":"branch length",
436 "display order":2
437 },
438 "Rate Distributions":{
439 "attribute type":"branch label",
440 "display order":3
441 },
442 "LRT":{
443 "attribute type":"branch label",
444 "display order":4
445 },
446 "Uncorrected P-value":{
447 "attribute type":"branch label",
448 "display order":5
449 },
450 "Corrected P-value":{
451 "attribute type":"branch label",
452 "display order":6
453 }
454 } 476 }
455 } 477 }
456 } 478 }