Mercurial > repos > iuc > hyphy_summary

comparison test-data/summary/nsp8.BUSTED.json @ 0:f304c108aa1f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
author iuc
date Wed, 09 Jun 2021 07:03:54 +0000
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comparison
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-1:000000000000 0:f304c108aa1f
1 {
2 "Evidence Ratios":{
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9 },
10 "Site Log Likelihood":{
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26 "analysis":{
27 "authors":"Sergei L Kosakovsky Pond",
28 "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
29 "contact":"spond@temple.edu",
30 "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted \njointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. \nAssuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio \nstyle analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, \nand relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2). Version 2.1 adds a grid search for the initial starting point.\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. Version 3.0 implements the option\nfor branch-site variation in synonymous substitution rates. Version 3.1 adds HMM auto-correlation option for SRV, and binds SRV distributions for multiple branch sets\n",
31 "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
32 "version":"3.1"
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237 "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":{
238 "MG94xREV with separate rates for branch sets":0.003464842721698225,
239 "Nucleotide GTR":0.003372774424770855,
240 "constrained":0.003508044185651234,
241 "original name":"gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human",
242 "unconstrained":0.003507815553802554
243 },
244 "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":{
245 "MG94xREV with separate rates for branch sets":0.001735902729262228,
246 "Nucleotide GTR":0.001686266012390882,
247 "constrained":0.001736374314870017,
248 "original name":"gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human",
249 "unconstrained":0.001735532172102446
250 },
251 "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":{
252 "MG94xREV with separate rates for branch sets":0.003480097445970276,
253 "Nucleotide GTR":0.003374436490976879,
254 "constrained":0.003479100177235689,
255 "original name":"gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human",
256 "unconstrained":0.003478891730919581
257 },
258 "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":{
259 "MG94xREV with separate rates for branch sets":0.00347257104743095,
260 "Nucleotide GTR":0.003376034743011948,
261 "constrained":0.003518997887784842,
262 "original name":"gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human",
263 "unconstrained":0.003517561264776653
264 },
265 "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":{
266 "MG94xREV with separate rates for branch sets":0.003474988463675508,
267 "Nucleotide GTR":0.003374190741831846,
268 "constrained":0.003517174184123671,
269 "original name":"gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human",
270 "unconstrained":0.00351929009659662
271 },
272 "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":{
273 "MG94xREV with separate rates for branch sets":0.003471294880555319,
274 "Nucleotide GTR":0.003376937492543959,
275 "constrained":0.003517915599429177,
276 "original name":"gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human",
277 "unconstrained":0.003516462270783854
278 }
279 },
280 "attributes":{
281 "MG94xREV with separate rates for branch sets":{
282 "attribute type":"branch length",
283 "display order":1
284 },
285 "Nucleotide GTR":{
286 "attribute type":"branch length",
287 "display order":0
288 },
289 "constrained":{
290 "attribute type":"branch length",
291 "display order":1
292 },
293 "original name":{
294 "attribute type":"node label",
295 "display order":0
296 },
297 "unconstrained":{
298 "attribute type":"branch length",
299 "display order":0
300 }
301 }
302 },
303 "data partitions":{
304 "0":{
305 "coverage": [
306 [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, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197]
307 ],
308 "name":"busted.filter.default"
309 }
310 },
311 "fits":{
312 "Constrained model":{
313 "AIC-c":2537.370055580011,
314 "Log Likelihood":-1205.042170647148,
315 "Rate Distributions":{
316 "Background":{
317 "0":{
318 "omega":0.00623371489168318,
319 "proportion":0.02824597255703105
320 },
321 "1":{
322 "omega":0.1719986773053319,
323 "proportion":0.8104926399157489
324 },
325 "2":{
326 "omega":2.233103409549535,
327 "proportion":0.16126138752722
328 }
329 },
330 "Synonymous site-to-site rates":{
331 "0":{
332 "proportion":0,
333 "rate":0.9507923294014373
334 },
335 "1":{
336 "proportion":1,
337 "rate":1
338 },
339 "2":{
340 "proportion":0,
341 "rate":1.059005087778388
342 }
343 },
344 "Test":{
345 "0":{
346 "omega":0.9993683385761363,
347 "proportion":2.155223602575912e-10
348 },
349 "1":{
350 "omega":0.999707726011995,
351 "proportion":2.155223602111413e-10
352 },
353 "2":{
354 "omega":1,
355 "proportion":0.9999999995689552
356 }
357 }
358 },
359 "display order":3,
360 "estimated parameters":63
361 },
362 "MG94xREV with separate rates for branch sets":{
363 "AIC-c":2512.962001126987,
364 "Equilibrium frequencies": [
365 [0.03825952761243274],
366 [0.01370948533169502],
367 [0.0238326285579188],
368 [0.05169206288834598],
369 [0.02910782227384961],
370 [0.01043016700423795],
371 [0.01813184740308045],
372 [0.03932728586627101],
373 [0.01035067712195123],
374 [0.003708944282165923],
375 [0.006447644771501305],
376 [0.01398469573761802],
377 [0.0283653688047424],
378 [0.01016412464618009],
379 [0.01766935821790241],
380 [0.03832416445281453],
381 [0.01521889661505549],
382 [0.005453366858635389],
383 [0.009480156518454269],
384 [0.02056209812326697],
385 [0.01157852606970437],
386 [0.004148917752546374],
387 [0.007212496554133422],
388 [0.01564363009947405],
389 [0.00411729822204095],
390 [0.001475345962268018],
391 [0.002564747797779777],
392 [0.005562840210150803],
393 [0.01128319250724396],
394 [0.004043091272315801],
395 [0.007028527343480687],
396 [0.01524460789411934],
397 [0.03592403244011121],
398 [0.01287261047188149],
399 [0.02237780168434643],
400 [0.04853659885475865],
401 [0.02733097915424774],
402 [0.009793473186905268],
403 [0.01702501611901085],
404 [0.03692661100139533],
405 [0.009718835644621534],
406 [0.003482537371104292],
407 [0.0060540580187001],
408 [0.01313102107355921],
409 [0.02663384763763138],
410 [0.009543670983435077],
411 [0.01659075888876379],
412 [0.0359847236220365],
413 [0.00848480075962617],
414 [0.03199221880690793],
415 [0.01801483181642438],
416 [0.006455230577911434],
417 [0.01122180073845716],
418 [0.02433965804833868],
419 [0.002295465694104339],
420 [0.003990447484454917],
421 [0.008655128485630147],
422 [0.01755532734880559],
423 [0.00629057695692368],
424 [0.01093556617204019],
425 [0.02371882618448924]
426 ],
427 "Log Likelihood":-1205.058976375078,
428 "Rate Distributions":{
429 "non-synonymous/synonymous rate ratio for *background*": [
430 [0.4929148114260853, 1]
431 ],
432 "non-synonymous/synonymous rate ratio for *test*": [
433 [24.31954749176878, 1]
434 ]
435 },
436 "display order":1,
437 "estimated parameters":51
438 },
439 "Nucleotide GTR":{
440 "AIC-c":2633.0046471406,
441 "Equilibrium frequencies": [
442 [0.3251262626262627],
443 [0.1799242424242424],
444 [0.2026515151515151],
445 [0.2922979797979798]
446 ],
447 "Log Likelihood":-1247.247280799152,
448 "Rate Distributions":{
449 "Substitution rate from nucleotide A to nucleotide C":0,
450 "Substitution rate from nucleotide A to nucleotide G":1,
451 "Substitution rate from nucleotide A to nucleotide T":0.3101631549852981,
452 "Substitution rate from nucleotide C to nucleotide G":1.129990583516242,
453 "Substitution rate from nucleotide C to nucleotide T":2.723444388603395,
454 "Substitution rate from nucleotide G to nucleotide T":1.720896006888861
455 },
456 "display order":0,
457 "estimated parameters":69
458 },
459 "Unconstrained model":{
460 "AIC-c":2538.426858070025,
461 "Log Likelihood":-1204.550057961818,
462 "Rate Distributions":{
463 "Background":{
464 "0":{
465 "omega":0,
466 "proportion":0.02741862862724963
467 },
468 "1":{
469 "omega":0.1719979491289183,
470 "proportion":0.8111826871363725
471 },
472 "2":{
473 "omega":2.232058479326601,
474 "proportion":0.1613986842363778
475 }
476 },
477 "Synonymous site-to-site rates":{
478 "0":{
479 "proportion":0,
480 "rate":0.9502886367487763
481 },
482 "1":{
483 "proportion":1,
484 "rate":1
485 },
486 "2":{
487 "proportion":0,
488 "rate":1.059678592887729
489 }
490 },
491 "Test":{
492 "0":{
493 "omega":0.9993684330797956,
494 "proportion":0
495 },
496 "1":{
497 "omega":0.999368433118802,
498 "proportion":0
499 },
500 "2":{
501 "omega":25.32658549655282,
502 "proportion":1
503 }
504 }
505 },
506 "display order":2,
507 "estimated parameters":64
508 }
509 },
510 "input":{
511 "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas",
512 "number of sequences":32,
513 "number of sites":198,
514 "partition count":1,
515 "trees":{
516 "0":"(REFERENCE,(gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human,epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021)Node20,gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human,epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021,(epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021,gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human)Node4,epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021,gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human,gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human,epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021,gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human,(gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human,gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human,epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021)Node38,epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021,gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human,epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021,gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human,epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021,epi_isl_1543980_hCoV_19_Singapore_490_2021,epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021,gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human,epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021,gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human,gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human,epi_isl_1652118_hCoV_19_Singapore_575_2021,epi_isl_1652105_hCoV_19_Singapore_561_2021,gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human,gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human,epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)"
517 }
518 },
519 "test results":{
520 "LRT":0.9842253706597148,
521 "p-value":0.3056667368082906
522 },
523 "tested":{
524 "0":{
525 "Node20":"test",
526 "Node38":"background",
527 "Node4":"test",
528 "REFERENCE":"background",
529 "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"background",
530 "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"background",
531 "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"background",
532 "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"background",
533 "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"background",
534 "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"background",
535 "epi_isl_1543980_hCoV_19_Singapore_490_2021":"background",
536 "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"background",
537 "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"background",
538 "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"background",
539 "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"background",
540 "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"background",
541 "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"background",
542 "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"background",
543 "epi_isl_1652105_hCoV_19_Singapore_561_2021":"background",
544 "epi_isl_1652118_hCoV_19_Singapore_575_2021":"background",
545 "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"background",
546 "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"background",
547 "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"background",
548 "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"background",
549 "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"background",
550 "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"background",
551 "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"background",
552 "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":"background",
553 "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":"background",
554 "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"background",
555 "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"background",
556 "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"background",
557 "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"background",
558 "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"background",
559 "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"background"
560 }
561 },
562 "timers":{
563 "Constrained BUSTED model fitting":{
564 "order":3,
565 "timer":3
566 },
567 "Overall":{
568 "order":0,
569 "timer":76
570 },
571 "Preliminary model fitting":{
572 "order":1,
573 "timer":6
574 },
575 "Unconstrained BUSTED model fitting":{
576 "order":2,
577 "timer":66
578 }
579 }
580 }