Mercurial > repos > iuc > hyphy_absrel
view test-data/fel-out1.json @ 12:107d3ba7024a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 16da4cfb8e771ea5e7dc2772c4fe2c160535838b"
author | iuc |
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date | Fri, 01 May 2020 13:45:18 -0400 |
parents | 419cd817299c |
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{ "analysis":{ "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 ", "version":"2.00", "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", "authors":"Sergei L Kosakovsky Pond and Simon DW Frost", "contact":"spond@temple.edu", "requirements":"in-frame codon alignment and a phylogenetic tree" }, "input":{ "file name":"/Users/stephenshank/Documents/Data/Datamonkey/CD2.fasta", "number of sequences":10, "number of sites":187, "partition count":1, "trees":{ "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.085099,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)" } }, "fits":{ "Nucleotide GTR":{ "Log Likelihood":-3531.963798530155, "estimated parameters":24, "AIC-c":7112.142458295762, "Equilibrium frequencies":[ [0.3563279857397504], [0.1837789661319073], [0.2402852049910873], [0.2196078431372549] ], "Rate Distributions":{ "Substitution rate from nucleotide A to nucleotide C":0.5474490057204714, "Substitution rate from nucleotide A to nucleotide G":1, "Substitution rate from nucleotide A to nucleotide T":0.2645352969683238, "Substitution rate from nucleotide C to nucleotide G":0.4863078374555331, "Substitution rate from nucleotide C to nucleotide T":1.018028772244997, "Substitution rate from nucleotide G to nucleotide T":0.3025951149895378 }, "display order":0 }, "Global MG94xREV":{ "Log Likelihood":-3466.725508616141, "estimated parameters":31, "AIC-c":6996.530451399855, "Equilibrium frequencies":[ [0.04785168648208005], [0.03911346079312019], [0.04842054060317301], [0.04069665666515385], [0.01817010744778396], [0.01485205303123071], [0.01838611113045968], [0.01545321970309948], [0.0190138898893362], [0.01554175184587827], [0.01923992433904378], [0.01617083546230154], [0.02796925133965702], [0.02286176927319543], [0.02830174586718859], [0.02378714529482007], [0.01687870337957799], [0.01379647304851128], [0.01707935503225849], [0.01435491300079667], [0.006409133648843443], [0.005238757839512795], [0.006485324528555602], [0.005450807083377185], [0.006706760641638982], [0.005482034985409045], [0.006786489669196017], [0.005703931360295163], [0.009865581170012171], [0.008064021368173151], [0.009982861811889655], [0.008390428826966174], [0.03287895020631181], [0.02687490503171972], [0.033269810543681], [0.0279627207822247], [0.01248470225271473], [0.01020486315060615], [0.01263311863778268], [0.01061792547971484], [0.01306446616325414], [0.01067875601941112], [0.01321977470017749], [0.01111100011404158], [0.01921770557551369], [0.01570834862514353], [0.01944616295744266], [0.01634417558076203], [0.01975257768318274], [0.02055210293142003], [0.009176034326710849], [0.007500393094996483], [0.00928511773266342], [0.007803986567571961], [0.00784869593340758], [0.009716299514778986], [0.008166387662818644], [0.01412467213650941], [0.01154535713247913], [0.01429258425298098], [0.01201267864744234] ], "Rate Distributions":{ "non-synonymous/synonymous rate ratio for *test*":[ [0.9970623081401093, 1] ] }, "display order":1 } }, "timers":{ "Total time":{ "timer":240, "order":0 }, "Model fitting":{ "timer":21, "order":1 }, "FEL analysis":{ "timer":208, "order":2 } }, "tested":{ "0":{ "Pig":"test", "Cow":"test", "Node3":"test", "Horse":"test", "Cat":"test", "Node2":"test", "RhMonkey":"test", "Baboon":"test", "Node9":"test", "Human":"test", "Chimp":"test", "Node12":"test", "Node8":"test", "Node1":"test", "Rat":"test", "Mouse":"test" } }, "data partitions":{ "0":{ "name":"fel.filter.default", "coverage":[ [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186] ] } }, "branch attributes":{ "0":{ "Human":{ "original name":"Human", "Nucleotide GTR":0, "Global MG94xREV":0 }, "Chimp":{ "original name":"Chimp", "Nucleotide GTR":0.001818647577470898, "Global MG94xREV":0.001828142895085465 }, "Baboon":{ "original name":"Baboon", "Nucleotide GTR":0.001683434956773037, "Global MG94xREV":0.001771624553208579 }, "RhMonkey":{ "original name":"RhMonkey", "Nucleotide GTR":0.003773669075849421, "Global MG94xREV":0.003717699096857038 }, "Cow":{ "original name":"Cow", "Nucleotide GTR":0.2483322373763571, "Global MG94xREV":0.2480141631033857 }, "Pig":{ "original name":"Pig", "Nucleotide GTR":0.187244836750842, "Global MG94xREV":0.1926081878751187 }, "Horse":{ "original name":"Horse", "Nucleotide GTR":0.2091766851769093, "Global MG94xREV":0.2111575880588217 }, "Cat":{ "original name":"Cat", "Nucleotide GTR":0.266381043956941, "Global MG94xREV":0.273601177885004 }, "Mouse":{ "original name":"Mouse", "Nucleotide GTR":0.1181831744338598, "Global MG94xREV":0.1201847378516324 }, "Rat":{ "original name":"Rat", "Nucleotide GTR":0.06669700444436912, "Global MG94xREV":0.0670850471739789 }, "Node1":{ "Nucleotide GTR":0.276880831396131, "Global MG94xREV":0.2843521449765504 }, "Node12":{ "Nucleotide GTR":0.01783434870161725, "Global MG94xREV":0.01788794906051452 }, "Node2":{ "Nucleotide GTR":0.06617535490721377, "Global MG94xREV":0.06447679597474805 }, "Node3":{ "Nucleotide GTR":0.09884524766349881, "Global MG94xREV":0.1017497956116402 }, "Node8":{ "Nucleotide GTR":0.1061610073141143, "Global MG94xREV":0.1093806684969149 }, "Node9":{ "Nucleotide GTR":0.02568007351415409, "Global MG94xREV":0.02593963430985144 } }, "attributes":{ "original name":{ "attribute type":"node label", "display order":-1 }, "Nucleotide GTR":{ "attribute type":"branch length", "display order":0 }, "Global MG94xREV":{ "attribute type":"branch length", "display order":1 } } }, "MLE":{ "headers":[ ["alpha", "Synonymous substitution rate at a site"], ["beta", "Non-synonymous substitution rate at a site"], ["alpha=beta", "The rate estimate under the neutral model"], ["LRT", "Likelihood ration test statistic for beta = alpha, versus beta &neq; alpha"], ["p-value", "Likelihood ration test statistic for beta = alpha, versus beta &neq; alpha"], ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"] ], "content":{ "0":[ [0, 14.33455339565208, 9.37022855225735, 0.6569588574406389, 0.4176356384633009, 18.37456124129265], [0, 0, 0, 0, 1, 0], [0, 0, 0, 0, 1, 0], [2.315835044497769, 2.0838655960337, 2.154020315716453, 0.006512178791247436, 0.9356820703077827, 3.703306642750085], [4.684867463043267, 1.485880867051272, 1.810965132247134, 0.6423258738872875, 0.4228698174598849, 3.992627467732306], [2.793615407104073, 2.83663095770452, 2.827255675657259, 0.0001827272778811562, 0.9892147919393014, 4.881168204504374], [5.731991535867913e-15, 9.748939806634132, 7.039642474362661, 1.427528676396967, 0.2321681836368463, 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