Mercurial > repos > iuc > hyphy_meme

annotate test-data/relax-out1.json @ 30:45a2366d777e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 9ef881c2d3d5f240cbff33667b55f72cb82d9896"
author iuc
date Tue, 05 Oct 2021 05:04:06 +0000
parents e0763df98352
children 5d8389d684bf
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rev   line source
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iuc
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diff changeset
1 {
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2 "analysis":0,
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3 "branch attributes":{
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4 "0":{
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5 "Baboon":{
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6 "General descriptive":0.001858767762813579,
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8 "Nucleotide GTR":0.001680040630127455,
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13 "original name":"Baboon"
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23 "original name":"Cat"
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25 "Chimp":{
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33 "original name":"Chimp"
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53 "original name":"Horse"
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55 "Human":{
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166 "attribute type":"branch length",
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167 "display order":1
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169 "Nucleotide GTR":{
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170 "attribute type":"branch length",
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173 "RELAX alternative":{
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200 "name":"relax.filter.default"
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204 "General descriptive":{
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207 "Rate Distributions":{
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217 "2":{
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223 "display order":4,
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291 "Log Likelihood":-3461.208149286616,
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292 "Rate Distributions":{
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293 "non-synonymous/synonymous rate ratio for *Reference*": [
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296 "non-synonymous/synonymous rate ratio for *Test*": [
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299 },
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300 "display order":1,
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301 "estimated parameters":32
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302 },
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303 "Nucleotide GTR":{
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304 "AIC-c":7112.857310169033,
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305 "Equilibrium frequencies": [
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311 "Log Likelihood":-3532.32122446679,
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312 "Rate Distributions":{
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313 "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,
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314 "Substitution rate from nucleotide A to nucleotide G":1,
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315 "Substitution rate from nucleotide A to nucleotide T":0.2647746107611847,
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316 "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032,
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317 "Substitution rate from nucleotide C to nucleotide T":1.02837595903795,
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318 "Substitution rate from nucleotide G to nucleotide T":0.304509117524575
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319 },
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320 "display order":0,
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321 "estimated parameters":24
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322 },
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323 "RELAX alternative":{
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324 "AIC-c":6931.922980697387,
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325 "Log Likelihood":-3429.234812770952,
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326 "Rate Distributions":{
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327 "Reference":{
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328 "0":{
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329 "omega":1.762268314739328e-19,
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330 "proportion":0.4504132080156107
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331 },
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332 "1":{
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333 "omega":1.762268314739328e-19,
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334 "proportion":0.08749553114962015
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335 },
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336 "2":{
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337 "omega":2.19971015101232,
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428 "display order":5,
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429 "estimated parameters":40
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431 },
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432 "input":{
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433 "file name":"/tmp/tmpbauyxvdv/job_working_directory/000/3/working/./input.fasta",
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434 "number of sequences":10,
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435 "number of sites":187,
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436 "partition count":1,
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437 "trees":{
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438 "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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440 },
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441 "test results":{
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442 "LRT":16.20300116404087,
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443 "p-value":5.690389451429301e-05,
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444 "relaxation or intensification parameter":2.344938789085876
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445 },
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446 "tested":{
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447 "0":{
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448 "Baboon":"Reference",
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449 "Cat":"Test",
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450 "Chimp":"Reference",
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451 "Cow":"Test",
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452 "Horse":"Test",
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453 "Human":"Reference",
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454 "Mouse":"Reference",
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455 "Node1":"Reference",
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456 "Node12":"Reference",
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457 "Node2":"Reference",
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458 "Node3":"Reference",
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459 "Node8":"Reference",
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460 "Node9":"Reference",
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461 "Pig":"Reference",
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462 "Rat":"Reference",
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463 "RhMonkey":"Reference"
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464 }
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465 },
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466 "timers":{
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467 "General descriptive model fitting":{
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468 "order":2,
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469 "timer":132
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470 },
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471 "Overall":{
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472 "order":0,
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473 "timer":324
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474 },
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475 "Preliminary model fitting":{
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476 "order":1,
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477 "timer":8
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478 },
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479 "RELAX alternative model fitting":{
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480 "order":3,
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481 "timer":65
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482 },
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483 "RELAX null model fitting":{
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484 "order":4,
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485 "timer":66
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486 },
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487 "RELAX partitioned descriptive":{
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488 "order":5,
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489 "timer":53
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492 }