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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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7 ]
8 },
9 "Synonymous site-posteriors": [
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13 ],
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,
29 "branch attributes":{
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179 }
180 },
181 "fits":{
182 "MG94xREV with separate rates for branch sets":{
183 "AIC-c":1127.910850580984,
184 "Equilibrium frequencies": [
185 [0.04024763514913952],
186 [0.01922996663172304],
187 [0.03420070900547616],
188 [0.014368896284083],
189 [0.03368306905822573],
190 [0.01609347460151461],
191 [0.02862242313127222],
192 [0.01202526618107644],
193 [0.03424262136543949],
194 [0.01636082378008254],
195 [0.02909790661151763],
196 [0.01222503317454278],
197 [0.04878002735358049],
198 [0.02330666869812213],
199 [0.04145116886040549],
200 [0.01741506429336918],
201 [0.01835841860430346],
202 [0.008771491191067078],
203 [0.0156001944004883],
204 [0.006554179193076294],
205 [0.01536407988586604],
206 [0.007340822446772941],
207 [0.01305573416590236],
208 [0.0054851637757677],
209 [0.0156193121609741],
210 [0.007462770186447074],
211 [0.01327261957388795],
212 [0.005576284808737427],
213 [0.02225035479396483],
214 [0.01063102412468302],
215 [0.01890739435390807],
216 [0.007943647847477694],
217 [0.02003764925766833],
218 [0.009573812850750063],
219 [0.01702713237376286],
220 [0.007153685002693248],
221 [0.01676942064321455],
222 [0.008012281919357385],
223 [0.01424993228754379],
224 [0.005986887554352669],
225 [0.01704799882132915],
226 [0.008145384126471394],
227 [0.01448665603962682],
228 [0.006086343359234239],
229 [0.02428557790460417],
230 [0.01160343585423386],
231 [0.0206368394035431],
232 [0.008670247303157035],
233 [0.01086675715317312],
234 [0.008119790817560615],
235 [0.01903413243710357],
236 [0.009094341326464849],
237 [0.01617438694822276],
238 [0.006795417266946891],
239 [0.009245418998841326],
240 [0.01644308026470771],
241 [0.006908304587387538],
242 [0.02756534742509875],
243 [0.0131704809291841],
244 [0.02342384645525713],
245 [0.009841164995614077]
246 ],
247 "Log Likelihood":-535.0231635224093,
248 "Rate Distributions":{
249 "non-synonymous/synonymous rate ratio for *background*": [
250 [0.2332468645873907, 1]
251 ],
252 "non-synonymous/synonymous rate ratio for *test*": [
253 [0.05436826671559885, 1]
254 ]
255 },
256 "display order":1,
257 "estimated parameters":28
258 },
259 "Nucleotide GTR":{
260 "AIC-c":1165.694393932368,
261 "Equilibrium frequencies": [
262 [0.3348148148148147],
263 [0.202962962962963],
264 [0.2462962962962963],
265 [0.2159259259259259]
266 ],
267 "Log Likelihood":-559.6409189392783,
268 "Rate Distributions":{
269 "Substitution rate from nucleotide A to nucleotide C":0.1057602468701381,
270 "Substitution rate from nucleotide A to nucleotide G":1,
271 "Substitution rate from nucleotide A to nucleotide T":0,
272 "Substitution rate from nucleotide C to nucleotide G":0.1465960735122673,
273 "Substitution rate from nucleotide C to nucleotide T":2.269319946484975,
274 "Substitution rate from nucleotide G to nucleotide T":0.1391184331291334
275 },
276 "display order":0,
277 "estimated parameters":23
278 },
279 "Unconstrained model":{
280 "AIC-c":1164.066233233619,
281 "Log Likelihood":-534.6092290289872,
282 "Rate Distributions":{
283 "Background":{
284 "0":{
285 "omega":236.9358471479831,
286 "proportion":0
287 },
288 "1":{
289 "omega":0.2100294329667581,
290 "proportion":0.5542688958966767
291 },
292 "2":{
293 "omega":0.255710153738319,
294 "proportion":0.4457311041033233
295 },
296 "3":{
297 "omega":0.2978621753285197,
298 "proportion":0
299 }
300 },
301 "Synonymous site-to-site rates":{
302 "0":{
303 "proportion":0.3409863833415702,
304 "rate":0
305 },
306 "1":{
307 "proportion":0.6590136166584298,
308 "rate":1.517419329012598
309 },
310 "2":{
311 "proportion":0,
312 "rate":1.52677760828329
313 }
314 },
315 "Test":{
316 "0":{
317 "omega":226.0589415365084,
318 "proportion":0
319 },
320 "1":{
321 "omega":0.04198616898833647,
322 "proportion":0.9147510556650086
323 },
324 "2":{
325 "omega":0.1430120656070995,
326 "proportion":0.08477641331245425
327 },
328 "3":{
329 "omega":1,
330 "proportion":0.0004725310225371633
331 }
332 }
333 },
334 "display order":2,
335 "estimated parameters":45
336 }
337 },
338 "input":{
339 "file name":"/home/dcallan-adm/Documents/veg/CAPHEINE/work/87/f4fe290e4b23b20d10420f0110f410/capsid_protein_C-nodups.fasta",
340 "number of sequences":9,
341 "number of sites":100,
342 "partition count":1,
343 "trees":{
344 "0":"(PP563828_1_2023_09_04,PP563831_1_2023_08_29,PP563880_1_2023_10_05,((PP564823_1_2023_10_06,PP563845_1_2023_10_22)Node4,(PP563884_1_2023_09_24,PP563838_1_2023_09_30,PP563839_1_2023_09_29)Node7)Node3,PP563832_1_2023_08_28)"
345 }
346 },
347 "runtime":"2.5.73",
348 "substitutions":{
349 "0":{
350 "0":{
351 "root":"ATG"
352 },
353 "1":{
354 "root":"AAC"
355 },
356 "10":{
357 "root":"CCG"
358 },
359 "11":{
360 "root":"TCT"
361 },
362 "12":{
363 "root":"TTC"
364 },
365 "13":{
366 "root":"AAT"
367 },
368 "14":{
369 "root":"ATG"
370 },
371 "15":{
372 "root":"CTG"
373 },
374 "16":{
375 "root":"AAA"
376 },
377 "17":{
378 "root":"CGC"
379 },
380 "18":{
381 "root":"GCG"
382 },
383 "19":{
384 "root":"AGA"
385 },
386 "2":{
387 "root":"AAC"
388 },
389 "20":{
390 "root":"AAC"
391 },
392 "21":{
393 "root":"CGC"
394 },
395 "22":{
396 "root":"GTG"
397 },
398 "23":{
399 "root":"TCA"
400 },
401 "24":{
402 "root":"ACT"
403 },
404 "25":{
405 "PP564823_1_2023_10_06":"GGT",
406 "root":"GTT"
407 },
408 "26":{
409 "Node7":"TCA",
410 "PP564823_1_2023_10_06":"TCA",
411 "root":"CCA"
412 },
413 "27":{
414 "root":"CAG"
415 },
416 "28":{
417 "root":"TTG"
418 },
419 "29":{
420 "root":"GCG"
421 },
422 "3":{
423 "root":"CAA"
424 },
425 "30":{
426 "root":"AAG"
427 },
428 "31":{
429 "root":"AGA"
430 },
431 "32":{
432 "root":"TTC"
433 },
434 "33":{
435 "root":"TCA"
436 },
437 "34":{
438 "PP563831_1_2023_08_29":"GAA",
439 "root":"AAA"
440 },
441 "35":{
442 "root":"GGA"
443 },
444 "36":{
445 "root":"TTG"
446 },
447 "37":{
448 "Node7":"CTT",
449 "root":"CTC"
450 },
451 "38":{
452 "PP563884_1_2023_09_24":"TTA",
453 "root":"TCA"
454 },
455 "39":{
456 "root":"GGC"
457 },
458 "4":{
459 "PP563845_1_2023_10_22":"CGA",
460 "root":"CGG"
461 },
462 "40":{
463 "Node4":"CAA",
464 "root":"CAG"
465 },
466 "41":{
467 "root":"GGA"
468 },
469 "42":{
470 "root":"CCC"
471 },
472 "43":{
473 "root":"ATG"
474 },
475 "44":{
476 "root":"AAA"
477 },
478 "45":{
479 "PP563880_1_2023_10_05":"CTA",
480 "PP564823_1_2023_10_06":"ATG",
481 "root":"CTG"
482 },
483 "46":{
484 "root":"GTG"
485 },
486 "47":{
487 "root":"ATG"
488 },
489 "48":{
490 "root":"GCT"
491 },
492 "49":{
493 "Node3":"TTC",
494 "root":"TTT"
495 },
496 "5":{
497 "PP564823_1_2023_10_06":"AAG",
498 "root":"AAA"
499 },
500 "50":{
501 "root":"ATA"
502 },
503 "51":{
504 "root":"GCA"
505 },
506 "52":{
507 "root":"TTC"
508 },
509 "53":{
510 "root":"CTA"
511 },
512 "54":{
513 "root":"AGA"
514 },
515 "55":{
516 "Node4":"TTT",
517 "root":"TTC"
518 },
519 "56":{
520 "root":"CTA"
521 },
522 "57":{
523 "root":"GCC"
524 },
525 "58":{
526 "root":"ATA"
527 },
528 "59":{
529 "Node3":"CCC",
530 "root":"CCT"
531 },
532 "6":{
533 "root":"AAG"
534 },
535 "60":{
536 "root":"CCA"
537 },
538 "61":{
539 "root":"ACA"
540 },
541 "62":{
542 "root":"GCA"
543 },
544 "63":{
545 "Node4":"GGA",
546 "root":"GGG"
547 },
548 "64":{
549 "root":"ATT"
550 },
551 "65":{
552 "root":"TTG"
553 },
554 "66":{
555 "root":"GCT"
556 },
557 "67":{
558 "root":"AGA"
559 },
560 "68":{
561 "root":"TGG"
562 },
563 "69":{
564 "Node4":"GGC",
565 "PP564823_1_2023_10_06":"AGC",
566 "root":"GGT"
567 },
568 "7":{
569 "root":"ACG"
570 },
571 "70":{
572 "root":"TCA"
573 },
574 "71":{
575 "root":"TTC"
576 },
577 "72":{
578 "root":"AAG"
579 },
580 "73":{
581 "root":"AAG"
582 },
583 "74":{
584 "root":"AAT"
585 },
586 "75":{
587 "root":"GGA"
588 },
589 "76":{
590 "root":"GCG"
591 },
592 "77":{
593 "root":"ATC"
594 },
595 "78":{
596 "root":"AAA"
597 },
598 "79":{
599 "root":"GTG"
600 },
601 "8":{
602 "PP564823_1_2023_10_06":"GGT",
603 "root":"GCT"
604 },
605 "80":{
606 "PP563838_1_2023_09_30":"CTG",
607 "PP564823_1_2023_10_06":"TTA",
608 "root":"CTA"
609 },
610 "81":{
611 "root":"CGG"
612 },
613 "82":{
614 "root":"GGT"
615 },
616 "83":{
617 "PP563832_1_2023_08_28":"TTT",
618 "root":"TTC"
619 },
620 "84":{
621 "PP564823_1_2023_10_06":"AAA",
622 "root":"AAG"
623 },
624 "85":{
625 "root":"AAA"
626 },
627 "86":{
628 "PP564823_1_2023_10_06":"GAG",
629 "root":"GAA"
630 },
631 "87":{
632 "root":"ATC"
633 },
634 "88":{
635 "root":"TCA"
636 },
637 "89":{
638 "root":"AGC"
639 },
640 "9":{
641 "root":"CGA"
642 },
643 "90":{
644 "root":"ATG"
645 },
646 "91":{
647 "PP563845_1_2023_10_22":"TTG",
648 "root":"CTG"
649 },
650 "92":{
651 "PP564823_1_2023_10_06":"AAC",
652 "root":"AAT"
653 },
654 "93":{
655 "root":"ATA"
656 },
657 "94":{
658 "root":"ATG"
659 },
660 "95":{
661 "PP564823_1_2023_10_06":"AAC",
662 "root":"AAT"
663 },
664 "96":{
665 "PP564823_1_2023_10_06":"AGG",
666 "root":"AGA"
667 },
668 "97":{
669 "root":"AGG"
670 },
671 "98":{
672 "root":"AAA"
673 },
674 "99":{
675 "root":"AGA"
676 }
677 }
678 },
679 "test results":{
680 "LRT":0,
681 "p-value":0.5
682 },
683 "tested":{
684 "0":{
685 "Node3":"test",
686 "Node4":"test",
687 "Node7":"test",
688 "PP563828_1_2023_09_04":"background",
689 "PP563831_1_2023_08_29":"background",
690 "PP563832_1_2023_08_28":"background",
691 "PP563838_1_2023_09_30":"background",
692 "PP563839_1_2023_09_29":"background",
693 "PP563845_1_2023_10_22":"background",
694 "PP563880_1_2023_10_05":"background",
695 "PP563884_1_2023_09_24":"background",
696 "PP564823_1_2023_10_06":"background"
697 }
698 },
699 "timers":{
700 "Overall":{
701 "order":0,
702 "timer":28
703 },
704 "Preliminary model fitting":{
705 "order":1,
706 "timer":2
707 },
708 "Unconstrained BUSTED model fitting":{
709 "order":2,
710 "timer":25
711 }
712 }
713 }