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comparison test-data/prime-out1.json @ 12:6efabd37807b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
author iuc
date Tue, 07 Oct 2025 20:44:41 +0000
parents d088a1cca4a7
children
comparison
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11:d088a1cca4a7 12:6efabd37807b
1 {
2 "MLE":{
3 "content":{
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55 ]
56 },
57 "headers": [
58 ["alpha;", "Synonymous substitution rate at a site"],
59 ["β", "Log of property independent non-synonymous rate a site"],
60 ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"],
61 ["PRIME LogL", "Site Log-likelihood under the PRIME model"],
62 ["FEL LogL", "Site Log-likelihood under the FEL model"],
63 ["p-value", "Omnibus p-value (any property is important)"],
64 ["λ1", "Importance for Factor I bipolar"],
65 ["p1", "p-value for non-zero effect of Factor I bipolar"],
66 ["LogL1", "Log likelihood when there is no effect of Factor I bipolar"],
67 ["λ2", "Importance for Factor II secondary structure"],
68 ["p2", "p-value for non-zero effect of Factor II secondary structure"],
69 ["LogL2", "Log likelihood when there is no effect of Factor II secondary structure"],
70 ["λ3", "Importance for Factor III volume"],
71 ["p3", "p-value for non-zero effect of Factor III volume"],
72 ["LogL3", "Log likelihood when there is no effect of Factor III volume"],
73 ["λ4", "Importance for Factor IV composition"],
74 ["p4", "p-value for non-zero effect of Factor IV composition"],
75 ["LogL4", "Log likelihood when there is no effect of Factor IV composition"],
76 ["λ5", "Importance for Factor V charge"],
77 ["p5", "p-value for non-zero effect of Factor V charge"],
78 ["LogL5", "Log likelihood when there is no effect of Factor V charge"]
79 ]
80 },
81 "analysis":{
82 "authors":"Sergei L. Kosakovsky Pond",
83 "citation":"TBD",
84 "contact":"spond@temple.edu",
85 "info":"PRIME (PRoperty Informed Model of Evolution). Given a set of N amino-acid properties,\n fit a site-level model where non-synonymous rates depend on how much a non-synonymous substitution changes the \n properties of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )- lambda_2 * diff_2 (X,Y) -...).\n When lambda_k > 0, changes in property k are disfavored and when lambda_k < 0 -- they are promoted.\n At each site, N tests are performed\n A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ",
86 "requirements":"in-frame codon alignment and a phylogenetic tree",
87 "version":"0.0.1"
88 },
89 "branch attributes":{
90 "0":{
91 "CHICKEN_CK_160_2005":{
92 "Global MG94xREV":0.006875905528136641,
93 "Nucleotide GTR":0.006740765844759078,
94 "original name":"CHICKEN_CK_160_2005"
95 },
96 "CHICKEN_HEBEI_326_2005":{
97 "Global MG94xREV":0.03000509055831138,
98 "Nucleotide GTR":0.02817726192677478,
99 "original name":"CHICKEN_HEBEI_326_2005"
100 },
101 "CHICKEN_HONGKONG_915_97":{
102 "Global MG94xREV":0,
103 "Nucleotide GTR":0,
104 "original name":"CHICKEN_HONGKONG_915_97"
105 },
106 "CK_HK_WF157_2003":{
107 "Global MG94xREV":0,
108 "Nucleotide GTR":0,
109 "original name":"CK_HK_WF157_2003"
110 },
111 "GOOSE_HONGKONG_W355_97":{
112 "Global MG94xREV":0,
113 "Nucleotide GTR":0,
114 "original name":"GOOSE_HONGKONG_W355_97"
115 },
116 "GOOSE_SHANTOU_2216_2005":{
117 "Global MG94xREV":0.008912012248907763,
118 "Nucleotide GTR":0.007985902570718373,
119 "original name":"GOOSE_SHANTOU_2216_2005"
120 },
121 "HONGKONG_1_538_97":{
122 "Global MG94xREV":0,
123 "Nucleotide GTR":0,
124 "original name":"HONGKONG_1_538_97"
125 },
126 "HONGKONG_1_97_98":{
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128 "Nucleotide GTR":0.02001220163799822,
129 "original name":"HONGKONG_1_97_98"
130 },
131 "HUMAN_VIETNAM_3062_2004":{
132 "Global MG94xREV":0,
133 "Nucleotide GTR":0,
134 "original name":"HUMAN_VIETNAM_3062_2004"
135 },
136 "HUMAN_VIETNAM_CL105_2005":{
137 "Global MG94xREV":0.006025788919462983,
138 "Nucleotide GTR":0.005802088014335368,
139 "original name":"HUMAN_VIETNAM_CL105_2005"
140 },
141 "MALLARD_VIETNAM_16_2003":{
142 "Global MG94xREV":0,
143 "Nucleotide GTR":0,
144 "original name":"MALLARD_VIETNAM_16_2003"
145 },
146 "Node10":{
147 "Global MG94xREV":0,
148 "Nucleotide GTR":0
149 },
150 "Node11":{
151 "Global MG94xREV":0,
152 "Nucleotide GTR":0
153 },
154 "Node13":{
155 "Global MG94xREV":0,
156 "Nucleotide GTR":0
157 },
158 "Node17":{
159 "Global MG94xREV":0,
160 "Nucleotide GTR":0
161 },
162 "Node18":{
163 "Global MG94xREV":0,
164 "Nucleotide GTR":0
165 },
166 "Node19":{
167 "Global MG94xREV":0.004922199772633382,
168 "Nucleotide GTR":0.005534464552270369
169 },
170 "Node2":{
171 "Global MG94xREV":0.006872306486383904,
172 "Nucleotide GTR":0.006718147482064949
173 },
174 "Node23":{
175 "Global MG94xREV":0,
176 "Nucleotide GTR":0
177 },
178 "Node24":{
179 "Global MG94xREV":0,
180 "Nucleotide GTR":0
181 },
182 "Node25":{
183 "Global MG94xREV":0.0008268367968756879,
184 "Nucleotide GTR":0.0009189593587976459
185 },
186 "Node3":{
187 "Global MG94xREV":0,
188 "Nucleotide GTR":0
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190 "Node4":{
191 "Global MG94xREV":0.002648185777377607,
192 "Nucleotide GTR":0.00251461257430795
193 },
194 "Node5":{
195 "Global MG94xREV":0.003268514528883674,
196 "Nucleotide GTR":0.003965274251091903
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198 "Node7":{
199 "Global MG94xREV":0.005023432525711092,
200 "Nucleotide GTR":0.004793454999477672
201 },
202 "Node9":{
203 "Global MG94xREV":0.01391813691986412,
204 "Nucleotide GTR":0.01351408611669037
205 },
206 "PEREGRINEFALCON_HK_D0028_2004":{
207 "Global MG94xREV":0.006920710269269024,
208 "Nucleotide GTR":0.006722811033712868,
209 "original name":"PEREGRINEFALCON_HK_D0028_2004"
210 },
211 "SWINE_ANHUI_1_2004":{
212 "Global MG94xREV":0.01018798286684916,
213 "Nucleotide GTR":0.009150633137551082,
214 "original name":"SWINE_ANHUI_1_2004"
215 }
216 },
217 "attributes":{
218 "Global MG94xREV":{
219 "attribute type":"branch length",
220 "display order":1
221 },
222 "Nucleotide GTR":{
223 "attribute type":"branch length",
224 "display order":0
225 },
226 "original name":{
227 "attribute type":"node label",
228 "display order":-1
229 }
230 }
231 },
232 "data partitions":{
233 "0":{
234 "coverage": [
235 [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]
236 ],
237 "name":"prime.filter.default"
238 }
239 },
240 "fits":{
241 "Global MG94xREV":{
242 "AIC-c":647.6795207053656,
243 "Equilibrium frequencies": [
244 [0.04488063522282697],
245 [0.02743154763030629],
246 [0.03260676907658289],
247 [0.05361444334761576],
248 [0.01878621141548667],
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252 [0.00898846188937465],
253 [0.005493848721556544],
254 [0.006530315351495689],
255 [0.01073762388516669],
256 [0.04007728102844568],
257 [0.02449568367218243],
258 [0.02911702655775225],
259 [0.04787635251947601],
260 [0.02154103095825152],
261 [0.01316611972632322],
262 [0.01565003299619046],
263 [0.02573293310637029],
264 [0.009016680795182521],
265 [0.005511096433290134],
266 [0.006550817007515099],
267 [0.01077133421300087],
268 [0.004314126457096238],
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270 [0.003134307802358531],
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272 [0.01923560009946569],
273 [0.01175701452767408],
274 [0.01397508674685076],
275 [0.02297886352699522],
276 [0.03843194498464033],
277 [0.02349003582808618],
278 [0.02792165371671785],
279 [0.04591083274306419],
280 [0.01608690786137961],
281 [0.00983249851595989],
282 [0.0116874925496928],
283 [0.01921743321791434],
284 [0.00769695150511784],
285 [0.004704463089092132],
286 [0.005592004637968804],
287 [0.00919478452948895],
288 [0.03431876246786721],
289 [0.02097601254029597],
290 [0.02493333610872543],
291 [0.04099722156245031],
292 [0.006131000492593795],
293 [0.01198292502502543],
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295 [0.002566324448628536],
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297 [0.005015832814718212],
298 [0.001227885122343091],
299 [0.001459537288103269],
300 [0.002399878352343215],
301 [0.008957344771016727],
302 [0.00547482958980595],
303 [0.006507708080284218],
304 [0.01070045135026252]
305 ],
306 "Log Likelihood":-277.7176481414617,
307 "Rate Distributions":{
308 "non-synonymous/synonymous rate ratio for *test*": [
309 [0.4074296362572946, 1]
310 ]
311 },
312 "display order":1,
313 "estimated parameters":43
314 },
315 "Nucleotide GTR":{
316 "AIC-c":658.4548031196325,
317 "Equilibrium frequencies": [
318 [0.3543689320388349],
319 [0.1790722761596548],
320 [0.2076591154261057],
321 [0.2588996763754045]
322 ],
323 "Log Likelihood":-292.5311130078037,
324 "Rate Distributions":{
325 "Substitution rate from nucleotide A to nucleotide C":0,
326 "Substitution rate from nucleotide A to nucleotide G":1,
327 "Substitution rate from nucleotide A to nucleotide T":0,
328 "Substitution rate from nucleotide C to nucleotide G":0,
329 "Substitution rate from nucleotide C to nucleotide T":1.816257034982832,
330 "Substitution rate from nucleotide G to nucleotide T":0
331 },
332 "display order":0,
333 "estimated parameters":36
334 }
335 },
336 "input":{
337 "file name":"/Users/sergei/Development/tools-iuc/tools/hyphy/test-data/prime-in1.fa",
338 "number of sequences":13,
339 "number of sites":50,
340 "partition count":1,
341 "trees":{
342 "0":"(((((CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516)Node7:0.002095219592954275)Node5:0.003887237703073042)Node4:0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-1,(GOOSE_HONGKONG_W355_97:-1)Node13:0.002899766890966483)Node11:0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716)Node10:0.000182535836694054,HONGKONG_1_538_97:-1)Node9:0.02096173714686362)Node3:0.003130608143291779,(((GOOSE_SHANTOU_2216_2005:0.006207842095177651)Node19:0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232)Node18:0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774)Node17:0.004655295319725731)Node2:0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001)Node25:0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184)Node24:0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072)Node23:0.0004125980823087554,CHICKEN_CK_160_2005:0.006168335080088849)"
343 }
344 },
345 "tested":{
346 "0":{
347 "CHICKEN_CK_160_2005":"test",
348 "CHICKEN_HEBEI_326_2005":"test",
349 "CHICKEN_HONGKONG_915_97":"test",
350 "CK_HK_WF157_2003":"test",
351 "GOOSE_HONGKONG_W355_97":"test",
352 "GOOSE_SHANTOU_2216_2005":"test",
353 "HONGKONG_1_538_97":"test",
354 "HONGKONG_1_97_98":"test",
355 "HUMAN_VIETNAM_3062_2004":"test",
356 "HUMAN_VIETNAM_CL105_2005":"test",
357 "MALLARD_VIETNAM_16_2003":"test",
358 "Node10":"test",
359 "Node11":"test",
360 "Node13":"test",
361 "Node17":"test",
362 "Node18":"test",
363 "Node19":"test",
364 "Node2":"test",
365 "Node23":"test",
366 "Node24":"test",
367 "Node25":"test",
368 "Node3":"test",
369 "Node4":"test",
370 "Node5":"test",
371 "Node7":"test",
372 "Node9":"test",
373 "PEREGRINEFALCON_HK_D0028_2004":"test",
374 "SWINE_ANHUI_1_2004":"test"
375 }
376 },
377 "timers":{
378 "Model fitting":{
379 "order":1,
380 "timer":3
381 },
382 "PRIME analysis":{
383 "order":2,
384 "timer":86
385 },
386 "Total time":{
387 "order":0,
388 "timer":89
389 }
390 }
391 }