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comparison test-data/BUSTED/gene2.json @ 0:dd2d60b55e0d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drhip commit 15c654c3d27df68a47483031961ace7f5b8d998d
author iuc
date Thu, 04 Dec 2025 15:05:26 +0000
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-1:000000000000 0:dd2d60b55e0d
1 {
2 "Evidence Ratios":{
3 },
4 "Site Log Likelihood":{
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8 },
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14 "analysis":{
15 "authors":"Sergei L Kosakovsky Pond",
16 "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71, *Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril*, Mol Biol Evol. 37(8):2430-2439",
17 "contact":"spond@temple.edu",
18 "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted jointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. Assuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio style analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, and relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2).\n \nVersion 2.1 adds a grid search for the initial starting point.\n\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. \n\nVersion 3.0 implements the option for branch-site variation in synonymous substitution rates. \n\nVersion 3.1 adds HMM auto-correlation option for SRV, and binds SRV distributions for multiple branch sets.\n\nVersion 4.0 adds support for multiple hits (MH), ancestral state reconstruction saved to JSON, and profiling of branch-site level support for selection / multiple hits.\n\nVersion 4.2 adds calculation of MH-attributable fractions of substitutions.\n\nVersion 4.5 adds an 'error absorption' component \n\nVersion 4.6 adds support for MSS-type models\n",
19 "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
20 "settings":{
21 "error-sink":1,
22 "mss":"No",
23 "multiple-hit":"None",
24 "srv":"Yes"
25 },
26 "version":"4.6"
27 },
28 "background":1,
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189 [0.01555076352482647],
190 [0.006472514015538997],
191 [0.01534294594175388],
192 [0.007378175514105413],
193 [0.01306580710473399],
194 [0.005438229413926055],
195 [0.01559207164907205],
196 [0.007497976053105356],
197 [0.01327795856827995],
198 [0.005526530758038588],
199 [0.02204519218088164],
200 [0.01060117775101382],
201 [0.01877333269084459],
202 [0.00781380661894053],
203 [0.02001283201397348],
204 [0.009623848489980729],
205 [0.0170426073132688],
206 [0.007093446860043523],
207 [0.01681485300040535],
208 [0.008085991904804354],
209 [0.0143192595888557],
210 [0.005959939409601683],
211 [0.01708787828271292],
212 [0.008217285364372072],
213 [0.0145517635478013],
214 [0.006056711836919557],
215 [0.02416007116849923],
216 [0.01161818898347029],
217 [0.02057432977490965],
218 [0.008563414755540757],
219 [0.01095174735555056],
220 [0.008072200842739543],
221 [0.01913496685581441],
222 [0.009201697278655068],
223 [0.01629503140027161],
224 [0.006782292004731834],
225 [0.009351106613197152],
226 [0.01655961626153459],
227 [0.006892417094094173],
228 [0.02749367841825353],
229 [0.0132212670023302],
230 [0.02341317633368553],
231 [0.009744994946783913]
232 ],
233 "Log Likelihood":-522.0390000538857,
234 "Rate Distributions":{
235 "non-synonymous/synonymous rate ratio for *background*": [
236 [0.2134874183278158, 1]
237 ],
238 "non-synonymous/synonymous rate ratio for *test*": [
239 [0.05375692390200871, 1]
240 ]
241 },
242 "display order":1,
243 "estimated parameters":26
244 },
245 "Nucleotide GTR":{
246 "AIC-c":1130.795872905925,
247 "Equilibrium frequencies": [
248 [0.3347619047619048],
249 [0.2033333333333333],
250 [0.2466666666666667],
251 [0.2152380952380952]
252 ],
253 "Log Likelihood":-546.2152441452704,
254 "Rate Distributions":{
255 "Substitution rate from nucleotide A to nucleotide C":0.1157280802219541,
256 "Substitution rate from nucleotide A to nucleotide G":1,
257 "Substitution rate from nucleotide A to nucleotide T":0,
258 "Substitution rate from nucleotide C to nucleotide G":0.1604122535118794,
259 "Substitution rate from nucleotide C to nucleotide T":2.313607104947681,
260 "Substitution rate from nucleotide G to nucleotide T":0.1528462357734212
261 },
262 "display order":0,
263 "estimated parameters":19
264 },
265 "Unconstrained model":{
266 "AIC-c":1135.480989915523,
267 "Log Likelihood":-521.8563486162983,
268 "Rate Distributions":{
269 "Background":{
270 "0":{
271 "omega":224.9667643065964,
272 "proportion":0
273 },
274 "1":{
275 "omega":0.1788885192362742,
276 "proportion":0.5465744472573087
277 },
278 "2":{
279 "omega":0.251168474136212,
280 "proportion":0.4534255527426913
281 },
282 "3":{
283 "omega":0.2024887349695371,
284 "proportion":0
285 }
286 },
287 "Synonymous site-to-site rates":{
288 "0":{
289 "proportion":0.2729752444117259,
290 "rate":0
291 },
292 "1":{
293 "proportion":0,
294 "rate":1.396781922073988e-08
295 },
296 "2":{
297 "proportion":0.7270247555882741,
298 "rate":1.375468981370307
299 }
300 },
301 "Test":{
302 "0":{
303 "omega":223.2365630647954,
304 "proportion":0
305 },
306 "1":{
307 "omega":0.02758628794594435,
308 "proportion":0.1008034141000489
309 },
310 "2":{
311 "omega":0.05377704583904181,
312 "proportion":0.8985911133771098
313 },
314 "3":{
315 "omega":1,
316 "proportion":0.0006054725228412919
317 }
318 }
319 },
320 "display order":2,
321 "estimated parameters":43
322 }
323 },
324 "input":{
325 "file name":"/home/dcallan-adm/Documents/veg/CAPHEINE/work/a4/7d2a9b33d4505019743b214dbd74ff/pretend_DENV1_ref.part_NC_001477.1__capsid_protein_C__95-394_DENV1-nodups.fasta",
326 "number of sequences":7,
327 "number of sites":100,
328 "partition count":1,
329 "trees":{
330 "0":"(PP564823_1_2023_10_06,((PP563832_1_2023_08_28,PP563830_1_2023_09_02,PP563831_1_2023_08_29)Node3,(PP563839_1_2023_09_29,PP563838_1_2023_09_30)Node8)Node2,PP563845_1_2023_10_22)"
331 }
332 },
333 "runtime":"2.5.73",
334 "substitutions":{
335 "0":{
336 "0":{
337 "root":"ATG"
338 },
339 "1":{
340 "root":"AAC"
341 },
342 "10":{
343 "root":"CCG"
344 },
345 "11":{
346 "root":"TCT"
347 },
348 "12":{
349 "root":"TTC"
350 },
351 "13":{
352 "root":"AAT"
353 },
354 "14":{
355 "root":"ATG"
356 },
357 "15":{
358 "root":"CTG"
359 },
360 "16":{
361 "root":"AAA"
362 },
363 "17":{
364 "root":"CGC"
365 },
366 "18":{
367 "root":"GCG"
368 },
369 "19":{
370 "root":"AGA"
371 },
372 "2":{
373 "root":"AAC"
374 },
375 "20":{
376 "root":"AAC"
377 },
378 "21":{
379 "root":"CGC"
380 },
381 "22":{
382 "root":"GTG"
383 },
384 "23":{
385 "root":"TCA"
386 },
387 "24":{
388 "root":"ACT"
389 },
390 "25":{
391 "PP564823_1_2023_10_06":"GGT",
392 "root":"GTT"
393 },
394 "26":{
395 "Node8":"TCA",
396 "PP564823_1_2023_10_06":"TCA",
397 "root":"CCA"
398 },
399 "27":{
400 "root":"CAG"
401 },
402 "28":{
403 "root":"TTG"
404 },
405 "29":{
406 "root":"GCG"
407 },
408 "3":{
409 "root":"CAA"
410 },
411 "30":{
412 "root":"AAG"
413 },
414 "31":{
415 "root":"AGA"
416 },
417 "32":{
418 "root":"TTC"
419 },
420 "33":{
421 "root":"TCA"
422 },
423 "34":{
424 "PP563831_1_2023_08_29":"GAA",
425 "root":"AAA"
426 },
427 "35":{
428 "root":"GGA"
429 },
430 "36":{
431 "root":"TTG"
432 },
433 "37":{
434 "Node8":"CTT",
435 "root":"CTC"
436 },
437 "38":{
438 "root":"TCA"
439 },
440 "39":{
441 "root":"GGC"
442 },
443 "4":{
444 "PP563845_1_2023_10_22":"CGA",
445 "root":"CGG"
446 },
447 "40":{
448 "Node2":"CAG",
449 "root":"CAA"
450 },
451 "41":{
452 "root":"GGA"
453 },
454 "42":{
455 "root":"CCC"
456 },
457 "43":{
458 "root":"ATG"
459 },
460 "44":{
461 "root":"AAA"
462 },
463 "45":{
464 "PP564823_1_2023_10_06":"ATG",
465 "root":"CTG"
466 },
467 "46":{
468 "root":"GTG"
469 },
470 "47":{
471 "root":"ATG"
472 },
473 "48":{
474 "root":"GCT"
475 },
476 "49":{
477 "Node3":"TTT",
478 "root":"TTC"
479 },
480 "5":{
481 "PP564823_1_2023_10_06":"AAG",
482 "root":"AAA"
483 },
484 "50":{
485 "root":"ATA"
486 },
487 "51":{
488 "root":"GCA"
489 },
490 "52":{
491 "root":"TTC"
492 },
493 "53":{
494 "root":"CTA"
495 },
496 "54":{
497 "root":"AGA"
498 },
499 "55":{
500 "Node2":"TTC",
501 "root":"TTT"
502 },
503 "56":{
504 "root":"CTA"
505 },
506 "57":{
507 "root":"GCC"
508 },
509 "58":{
510 "root":"ATA"
511 },
512 "59":{
513 "Node3":"CCT",
514 "root":"CCC"
515 },
516 "6":{
517 "root":"AAG"
518 },
519 "60":{
520 "root":"CCA"
521 },
522 "61":{
523 "root":"ACA"
524 },
525 "62":{
526 "root":"GCA"
527 },
528 "63":{
529 "Node2":"GGG",
530 "root":"GGA"
531 },
532 "64":{
533 "root":"ATT"
534 },
535 "65":{
536 "root":"TTG"
537 },
538 "66":{
539 "root":"GCT"
540 },
541 "67":{
542 "root":"AGA"
543 },
544 "68":{
545 "root":"TGG"
546 },
547 "69":{
548 "Node2":"GGT",
549 "PP564823_1_2023_10_06":"AGC",
550 "root":"GGC"
551 },
552 "7":{
553 "root":"ACG"
554 },
555 "70":{
556 "root":"TCA"
557 },
558 "71":{
559 "root":"TTC"
560 },
561 "72":{
562 "root":"AAG"
563 },
564 "73":{
565 "root":"AAG"
566 },
567 "74":{
568 "root":"AAT"
569 },
570 "75":{
571 "root":"GGA"
572 },
573 "76":{
574 "root":"GCG"
575 },
576 "77":{
577 "root":"ATC"
578 },
579 "78":{
580 "root":"AAA"
581 },
582 "79":{
583 "root":"GTG"
584 },
585 "8":{
586 "PP564823_1_2023_10_06":"GGT",
587 "root":"GCT"
588 },
589 "80":{
590 "PP563838_1_2023_09_30":"CTG",
591 "PP564823_1_2023_10_06":"TTA",
592 "root":"CTA"
593 },
594 "81":{
595 "root":"CGG"
596 },
597 "82":{
598 "root":"GGT"
599 },
600 "83":{
601 "PP563832_1_2023_08_28":"TTT",
602 "root":"TTC"
603 },
604 "84":{
605 "PP564823_1_2023_10_06":"AAA",
606 "root":"AAG"
607 },
608 "85":{
609 "root":"AAA"
610 },
611 "86":{
612 "PP564823_1_2023_10_06":"GAG",
613 "root":"GAA"
614 },
615 "87":{
616 "root":"ATC"
617 },
618 "88":{
619 "root":"TCA"
620 },
621 "89":{
622 "root":"AGC"
623 },
624 "9":{
625 "root":"CGA"
626 },
627 "90":{
628 "root":"ATG"
629 },
630 "91":{
631 "PP563845_1_2023_10_22":"TTG",
632 "root":"CTG"
633 },
634 "92":{
635 "PP564823_1_2023_10_06":"AAC",
636 "root":"AAT"
637 },
638 "93":{
639 "root":"ATA"
640 },
641 "94":{
642 "root":"ATG"
643 },
644 "95":{
645 "PP564823_1_2023_10_06":"AAC",
646 "root":"AAT"
647 },
648 "96":{
649 "PP564823_1_2023_10_06":"AGG",
650 "root":"AGA"
651 },
652 "97":{
653 "root":"AGG"
654 },
655 "98":{
656 "root":"AAA"
657 },
658 "99":{
659 "root":"AGA"
660 }
661 }
662 },
663 "test results":{
664 "LRT":0,
665 "p-value":0.5
666 },
667 "tested":{
668 "0":{
669 "Node2":"test",
670 "Node3":"test",
671 "Node8":"test",
672 "PP563830_1_2023_09_02":"background",
673 "PP563831_1_2023_08_29":"background",
674 "PP563832_1_2023_08_28":"background",
675 "PP563838_1_2023_09_30":"background",
676 "PP563839_1_2023_09_29":"background",
677 "PP563845_1_2023_10_22":"background",
678 "PP564823_1_2023_10_06":"background"
679 }
680 },
681 "timers":{
682 "Overall":{
683 "order":0,
684 "timer":30
685 },
686 "Preliminary model fitting":{
687 "order":1,
688 "timer":2
689 },
690 "Unconstrained BUSTED model fitting":{
691 "order":2,
692 "timer":26
693 }
694 }
695 }