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comparison test-data/relax-out1.json @ 25:d88bbb287923 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author iuc
date Tue, 27 Apr 2021 18:01:09 +0000
parents bf97cacc1a55
children 5b6b8b08f1a9
comparison
equal deleted inserted replaced
24:e14d926dfdc4 25:d88bbb287923
1 { 1 {
2 "analysis":{ 2 "analysis":0,
3 "info":"RELAX (a random effects test of selection relaxation) uses a random effects branch-site model framework to test whether a set of 'Test' branches evolves under relaxed selection relative to a set of 'Reference' branches (R), as measured by the relaxation parameter (K).\n Version 2.1 adds a check for stability in K estimates to try to mitigate convergence problems", 3 "branch attributes":{
4 "version":"2.1", 4 "0":{
5 "citation":"RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015). Mol Biol Evol 32 (3): 820-832", 5 "Baboon":{
6 "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group", 6 "General descriptive":0.001858767762813579,
7 "contact":"spond@temple.edu", 7 "MG94xREV with separate rates for branch sets":0.001769472024099301,
8 "requirements":"in-frame codon alignment and a phylogenetic tree, with at least two groups of branches defined using the {} notation (one group can be defined as all unlabeled branches)" 8 "Nucleotide GTR":0.001680040630127455,
9 "RELAX alternative":0.001872256662230973,
10 "RELAX null":0.001855569334462731,
11 "RELAX partitioned descriptive":0.001898170574782418,
12 "k (general descriptive)":0.09971581394819819,
13 "original name":"Baboon"
14 },
15 "Cat":{
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22 "k (general descriptive)":2.314507643873676,
23 "original name":"Cat"
24 },
25 "Chimp":{
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27 "MG94xREV with separate rates for branch sets":0.001825434296531533,
28 "Nucleotide GTR":0.001818373670119325,
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30 "RELAX null":0.00183525802483954,
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32 "k (general descriptive)":5.261186652622472,
33 "original name":"Chimp"
34 },
35 "Cow":{
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43 "original name":"Cow"
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54 },
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60 "RELAX null":0,
61 "RELAX partitioned descriptive":0,
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63 "original name":"Human"
64 },
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73 "original name":"Mouse"
74 },
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148 },
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157 "original name":"RhMonkey"
158 }
159 },
160 "attributes":{
161 "General descriptive":{
162 "attribute type":"branch length",
163 "display order":4
164 },
165 "MG94xREV with separate rates for branch sets":{
166 "attribute type":"branch length",
167 "display order":1
168 },
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171 "display order":0
172 },
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176 },
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180 },
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185 "k (general descriptive)":{
186 "attribute type":"branch label",
187 "display order":4
188 },
189 "original name":{
190 "attribute type":"node label",
191 "display order":-1
192 }
193 }
194 },
195 "data partitions":{
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197 "coverage": [
198 [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]
199 ],
200 "name":"relax.filter.default"
201 }
202 },
203 "fits":{
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206 "Log Likelihood":-3420.486931066253,
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224 "estimated parameters":51
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292 "Rate Distributions":{
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296 "non-synonymous/synonymous rate ratio for *Test*": [
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428 "display order":5,
429 "estimated parameters":40
430 }
9 }, 431 },
10 "input":{ 432 "input":{
11 "file name":"/home/galaxystaging/galaxy/database/jobs_directory/000/79/working/relax_input.fa", 433 "file name":"/tmp/tmpbauyxvdv/job_working_directory/000/3/working/./input.fasta",
12 "number of sequences":10, 434 "number of sequences":10,
13 "number of sites":187, 435 "number of sites":187,
14 "partition count":1, 436 "partition count":1,
15 "trees":{ 437 "trees":{
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17 }
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111 "non-synonymous/synonymous rate ratio for *Test*":[
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253 "Preliminary model fitting":{
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256 },
257 "General descriptive model fitting":{
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260 },
261 "RELAX alternative model fitting":{
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264 },
265 "RELAX null model fitting":{
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269 "RELAX partitioned descriptive":{
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271 "order":5
272 } 439 }
273 }, 440 },
274 "test results":{ 441 "test results":{
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276 "p-value":5.932080525117289e-05, 443 "p-value":5.690389451429301e-05,
277 "relaxation or intensification parameter":0.4215604262166031 444 "relaxation or intensification parameter":2.344938789085876
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279 "tested":{ 446 "tested":{
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282 "Cow":"Reference", 449 "Cat":"Test",
283 "Node3":"Test", 450 "Chimp":"Reference",
284 "Horse":"Reference", 451 "Cow":"Test",
285 "Cat":"Reference", 452 "Horse":"Test",
286 "Node2":"Test", 453 "Human":"Reference",
287 "RhMonkey":"Test", 454 "Mouse":"Reference",
288 "Baboon":"Test", 455 "Node1":"Reference",
289 "Node9":"Test", 456 "Node12":"Reference",
290 "Human":"Test", 457 "Node2":"Reference",
291 "Chimp":"Test", 458 "Node3":"Reference",
292 "Node12":"Test", 459 "Node8":"Reference",
293 "Node8":"Test", 460 "Node9":"Reference",
294 "Node1":"Test", 461 "Pig":"Reference",
295 "Rat":"Test", 462 "Rat":"Reference",
296 "Mouse":"Test" 463 "RhMonkey":"Reference"
297 } 464 }
298 }, 465 },
299 "data partitions":{ 466 "timers":{
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302 "coverage":[ 469 "timer":132
303 [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] 470 },
304 ] 471 "Overall":{
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306 }, 473 "timer":324
307 "branch attributes":{ 474 },
308 "0":{ 475 "Preliminary model fitting":{
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310 "original name":"Human", 477 "timer":8
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316 "RELAX null":0, 483 "RELAX null model fitting":{
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497 } 490 }
498 } 491 }
499 } 492 }