Mercurial > repos > iuc > hyphy_summary

annotate test-data/relax-out2-1.json @ 6:81b23515db14 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author iuc
date Wed, 30 Mar 2022 00:23:34 +0000
parents f304c108aa1f
children f3e408cc2546
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0
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
1 {
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iuc
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diff changeset
2 "Synonymous site-posteriors": [
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81b23515db14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
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diff changeset
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81b23515db14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
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81b23515db14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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7 "analysis":0,
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8 "branch attributes":{
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9 "0":{
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10 "BABOON":{
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11 "General descriptive":0.001859562666773025,
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12 "MG94xREV with separate rates for branch sets":0.001729040005725717,
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13 "Nucleotide GTR":0.001685167654714891,
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14 "RELAX alternative":0.001434762988174167,
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15 "RELAX null":0.001618077326700096,
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16 "RELAX partitioned descriptive":0.001426437398554912,
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17 "k (general descriptive)":0.09975760133237818,
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18 "original name":"BABOON"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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20 "CAT":{
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21 "General descriptive":0.3649705108927348,
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23 "Nucleotide GTR":0.2660536011315811,
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24 "RELAX alternative":0.3757111787573828,
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25 "RELAX null":0.360767755751942,
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205 "name":"relax.filter.default"
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296 "Log Likelihood":-3461.064187903018,
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297 "Rate Distributions":{
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298 "non-synonymous/synonymous rate ratio for *Reference*": [
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299 [1.243401858007084, 1]
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300 ],
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301 "non-synonymous/synonymous rate ratio for *Test*": [
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308 "Nucleotide GTR":{
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310 "Equilibrium frequencies": [
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317 "Rate Distributions":{
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318 "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,
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319 "Substitution rate from nucleotide A to nucleotide G":1,
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320 "Substitution rate from nucleotide A to nucleotide T":0.2646800222727828,
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321 "Substitution rate from nucleotide C to nucleotide G":0.4918071762416347,
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322 "Substitution rate from nucleotide C to nucleotide T":1.028675134787727,
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325 "display order":0,
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326 "estimated parameters":24
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328 "RELAX alternative":{
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329 "AIC-c":6909.668413948684,
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330 "Log Likelihood":-3408.69933855329,
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331 "Rate Distributions":{
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332 "Reference":{
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333 "0":{
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334 "omega":0,
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335 "proportion":0.3825895192221547
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341 "2":{
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343 "proportion":0.6174104807778453
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344 }
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346 "Synonymous site-to-site rates":{
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347 "0":{
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348 "proportion":0.2789425737851868,
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349 "rate":0.2834765074731829
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350 },
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351 "1":{
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352 "proportion":0.6311785441975573,
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353 "rate":0.9970973177052372
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355 "2":{
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357 "rate":3.244142488658602
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358 }
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359 },
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360 "Test":{
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361 "0":{
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362 "omega":0,
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364 },
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365 "1":{
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366 "omega":0.9998114377116485,
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368 },
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369 "2":{
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370 "omega":1.000029443594731,
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371 "proportion":0.6174104807778453
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372 }
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373 }
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374 },
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375 "display order":2,
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376 "estimated parameters":45
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377 },
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378 "RELAX null":{
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379 "AIC-c":6919.152853316747,
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iuc
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diff changeset
380 "Log Likelihood":-3414.491495151524,
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381 "Rate Distributions":{
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471 "0":"((((PIG:0.147969,COW:0.21343)Node3:0.08509899999999999,HORSE:0.165787,CAT:0.264806)Node2:0.058611,((RHMONKEY:0.002015,BABOON:0.003108)Node9:0.022733,(HUMAN:0.004349,CHIMP:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,RAT:0.050958,MOUSE:0.09795)"
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474 "runtime":"2.5.32",
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475 "test results":{
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81b23515db14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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476 "LRT":11.58431319646934,
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477 "p-value":0.0006651049394417186,
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478 "relaxation or intensification parameter":3.335337302186161e-05
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479 },
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480 "tested":{
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481 "0":{
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482 "BABOON":"Test",
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483 "CAT":"Reference",
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484 "CHIMP":"Test",
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485 "COW":"Reference",
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486 "HORSE":"Reference",
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487 "HUMAN":"Test",
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488 "MOUSE":"Reference",
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489 "Node1":"Test",
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490 "Node12":"Test",
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491 "Node2":"Reference",
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492 "Node3":"Reference",
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493 "Node8":"Test",
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494 "Node9":"Test",
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495 "PIG":"Reference",
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496 "RAT":"Reference",
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497 "RHMONKEY":"Test"
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diff changeset
498 }
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499 },
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500 "timers":{
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501 "General descriptive model fitting":{
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502 "order":2,
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503 "timer":105
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504 },
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505 "Overall":{
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506 "order":0,
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507 "timer":3013
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508 },
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509 "Preliminary model fitting":{
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510 "order":1,
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511 "timer":8
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512 },
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513 "RELAX alternative model fitting":{
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514 "order":3,
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515 "timer":1229
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516 },
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517 "RELAX null model fitting":{
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518 "order":4,
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519 "timer":690
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520 },
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521 "RELAX partitioned descriptive":{
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522 "order":5,
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523 "timer":980
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524 }
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525 }
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526 }