Mercurial > repos > iuc > sarscov2summary

comparison test-data/fel.json @ 0:4ad8b610ea41 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
author iuc
date Mon, 04 May 2020 05:42:35 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:4ad8b610ea41
1 {
2 "MLE":{
3 "content":{
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1279 },
1280 "headers": [
1281 ["alpha", "Synonymous substitution rate at a site"],
1282 ["beta", "Non-synonymous substitution rate at a site"],
1283 ["alpha=beta", "The rate estimate under the neutral model"],
1284 ["LRT", "Likelihood ration test statistic for beta = alpha, versus beta &neq; alpha"],
1285 ["p-value", "Asymptotic p-value for evidence of selection, i.e. beta &neq; alpha"],
1286 ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
1287 ]
1288 },
1289 "analysis":{
1290 "authors":"Sergei L Kosakovsky Pond and Simon DW Frost",
1291 "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222",
1292 "contact":"spond@temple.edu",
1293 "info":"FEL (Fixed Effects Likelihood)\n estimates site-wise synonymous (α) and non-synonymous (β) rates, and\n uses a likelihood ratio test to determine if beta &neq; alpha at a site.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ",
1294 "requirements":"in-frame codon alignment and a phylogenetic tree",
1295 "version":"2.1"
1296 },
1297 "branch attributes":{
1298 "0":{
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1300 "Global MG94xREV":0,
1301 "Nucleotide GTR":0,
1302 "original name":"MN988713"
1303 },
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1305 "Global MG94xREV":0,
1306 "Nucleotide GTR":0,
1307 "original name":"MT263436"
1308 },
1309 "MT263450":{
1310 "Global MG94xREV":0.0002667411205297255,
1311 "Nucleotide GTR":0.0002618730591933583,
1312 "original name":"MT263450"
1313 },
1314 "MT263469":{
1315 "Global MG94xREV":0.0002668277258955213,
1316 "Nucleotide GTR":0.0002619448078896464,
1317 "original name":"MT263469"
1318 },
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1320 "Global MG94xREV":0,
1321 "Nucleotide GTR":0,
1322 "original name":"MT292570"
1323 },
1324 "MT292573":{
1325 "Global MG94xREV":0.0002669416362666168,
1326 "Nucleotide GTR":0.0002619663648691002,
1327 "original name":"MT292573"
1328 },
1329 "MT293207":{
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1331 "Nucleotide GTR":0.0002618218819513519,
1332 "original name":"MT293207"
1333 },
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1336 "Nucleotide GTR":0.000261818318230699,
1337 "original name":"MT345866"
1338 },
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1341 "Nucleotide GTR":0.0002618371209939757,
1342 "original name":"MT350282"
1343 },
1344 "MultiSeq0_24":{
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1347 "original name":"MultiSeq0_24"
1348 },
1349 "MultiSeq1_15":{
1350 "Global MG94xREV":0,
1351 "Nucleotide GTR":0,
1352 "original name":"MultiSeq1_15"
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1357 }
1358 },
1359 "attributes":{
1360 "Global MG94xREV":{
1361 "attribute type":"branch length",
1362 "display order":1
1363 },
1364 "Nucleotide GTR":{
1365 "attribute type":"branch length",
1366 "display order":0
1367 },
1368 "original name":{
1369 "attribute type":"node label",
1370 "display order":-1
1371 }
1372 }
1373 },
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1378 ],
1379 "name":"fel.filter.default"
1380 }
1381 },
1382 "fits":{
1383 "Global MG94xREV":{
1384 "AIC-c":10149.61180689111,
1385 "Equilibrium frequencies": [
1386 [0.02979562154488283],
1387 [0.01517388923390958],
1388 [0.01130216885195963],
1389 [0.04418850778207514],
1390 [0.02095495712216078],
1391 [0.01067164173078312],
1392 [0.007948700225080891],
1393 [0.03107732740096775],
1394 [0.01459620058968205],
1395 [0.007433344884251915],
1396 [0.005536676703090671],
1397 [0.02164694978335385],
1398 [0.02506836205256218],
1399 [0.0127664579336976],
1400 [0.009509009917223031],
1401 [0.03717772794149901],
1402 [0.01604345812288003],
1403 [0.00817038356185114],
1404 [0.006085654981252598],
1405 [0.0237933104716869],
1406 [0.01128320067261262],
1407 [0.005746147532190073],
1408 [0.004279979157350846],
1409 [0.01673359288637114],
1410 [0.007859327000813585],
1411 [0.00400248597545707],
1412 [0.00298122463034224],
1413 [0.01165580425345982],
1414 [0.01349806434457642],
1415 [0.006874101717537849],
1416 [0.005120128209683852],
1417 [0.02001835472486404],
1418 [0.0282479035525974],
1419 [0.01438568948634293],
1420 [0.01071508359657485],
1421 [0.0418931588347964],
1422 [0.01986646282387325],
1423 [0.01011730887724364],
1424 [0.007535809145258669],
1425 [0.02946303186770731],
1426 [0.01383800857688485],
1427 [0.007047223668324623],
1428 [0.00524907692478322],
1429 [0.02052251028786194],
1430 [0.02376619908450893],
1431 [0.01210331094708498],
1432 [0.009015069365738402],
1433 [0.0352465502897533],
1434 [0.01473791109327413],
1435 [0.04291887788275893],
1436 [0.02035287659406526],
1437 [0.0103650227455254],
1438 [0.007720317146018015],
1439 [0.03018440962574672],
1440 [0.00721976906124565],
1441 [0.005377596194652617],
1442 [0.02102498683295317],
1443 [0.02434809464399112],
1444 [0.01239965041937913],
1445 [0.009235795819038476],
1446 [0.03610953267190635]
1447 ],
1448 "Log Likelihood":-5046.747795530857,
1449 "Rate Distributions":{
1450 "non-synonymous/synonymous rate ratio for *background*": [
1451 [0.1424565175154827, 1]
1452 ],
1453 "non-synonymous/synonymous rate ratio for *test*": [
1454 [18.00630653685578, 1]
1455 ]
1456 },
1457 "display order":1,
1458 "estimated parameters":28
1459 },
1460 "Nucleotide GTR":{
1461 "AIC-c":10521.28687406032,
1462 "Equilibrium frequencies": [
1463 [0.294020328977124],
1464 [0.1892451617510534],
1465 [0.1841629174700659],
1466 [0.3325715918017568]
1467 ],
1468 "Log Likelihood":-5233.62542888362,
1469 "Rate Distributions":{
1470 "Substitution rate from nucleotide A to nucleotide C":0,
1471 "Substitution rate from nucleotide A to nucleotide G":1,
1472 "Substitution rate from nucleotide A to nucleotide T":0.1847803064876015,
1473 "Substitution rate from nucleotide C to nucleotide G":0,
1474 "Substitution rate from nucleotide C to nucleotide T":0.5743828140832303,
1475 "Substitution rate from nucleotide G to nucleotide T":0.2950953831288027
1476 },
1477 "display order":0,
1478 "estimated parameters":27
1479 }
1480 },
1481 "input":{
1482 "file name":"/galaxy-repl/main/jobdir/028/157/28157300/working/./fel_input.fa",
1483 "number of sequences":11,
1484 "number of sites":1273,
1485 "partition count":1,
1486 "trees":{
1487 "0":"(MN988713,MT292573,MT263469,MT350282,MultiSeq0_24,(MT292570,MT293207,MT345866,MT263436,MultiSeq1_15)Node6,MT263450)"
1488 }
1489 },
1490 "tested":{
1491 "0":{
1492 "MN988713":"background",
1493 "MT263436":"background",
1494 "MT263450":"background",
1495 "MT263469":"background",
1496 "MT292570":"background",
1497 "MT292573":"background",
1498 "MT293207":"background",
1499 "MT345866":"background",
1500 "MT350282":"background",
1501 "MultiSeq0_24":"background",
1502 "MultiSeq1_15":"background",
1503 "Node6":"test"
1504 }
1505 },
1506 "timers":{
1507 "FEL analysis":{
1508 "order":2,
1509 "timer":4
1510 },
1511 "Model fitting":{
1512 "order":1,
1513 "timer":7
1514 },
1515 "Total time":{
1516 "order":0,
1517 "timer":11
1518 }
1519 }
1520 }