Mercurial > repos > iuc > hyphy_annotate

comparison test-data/absrel-out2.json @ 9:88ea681b19d1 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 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author iuc
date Tue, 29 Mar 2022 23:59:39 +0000
parents
children
comparison
equal deleted inserted replaced
8:a016c2cb962d 9:88ea681b19d1
1 {
2 "Synonymous site-posteriors": [
3 [0.2237313836650769, 0.07034985497742986, 0.07145045464678079, 0.162904629542773, 0.08696014489632299, 0.4973049561752621, 0.9385366945295869, 0.07695133428552869, 0.001997373788362212, 0.000990883865044414, 1.597366276160643e-05, 0.001639173387605954, 0.0006726936008082838, 0.0005936260958686961, 0.01218331055979857, 6.818341915747173e-05, 3.10538784980663e-05, 0.0003850280284965983, 1.706749658825067e-05, 1.954717668341298e-05, 5.757139486184149e-05, 5.547696233589325e-07, 0.1027014607202221, 0.0005061229953062066, 0.0002713590976491243, 0.01071054750911007, 0.01058998805403938, 0.001824707456373813, 0.1040310240977791, 0.007394679956619656, 0.01548570716335477, 0.0008559908124777675, 0.0001902341284497764, 0.04379131907975038, 0.0001602246750758031, 0.872186620749095, 0.007390732327759301, 0.06674897008912457, 0.06972624550033353, 0.09402374412106476, 0.1105108657459435, 0.01328650075574577, 0.0004656132149530012, 0.02510551997724948, 2.726156324850206e-05, 0.218781542689419, 0.006387422790697847, 0.007440221639665756, 0.05243297879242407, 0.1290026685674839, 0.6362466982390221, 0.8443663408237136, 0.0008463748207276134, 0.07321341035497612, 0.7855063534903601, 0.3150726276771443, 0.8508489144151971, 0.02756928287263707, 0.01299322935453241, 0.01615676639466097, 0.1381872019916541, 0.06580359020038734, 0.007948607169236543, 0.03623393203353259, 0.001127119071510586, 2.510588082439908e-07, 0.001198735279712407, 1.499028692444743e-05, 0.0007376828878749214, 0.0001439329508670455, 0.0003622577009774282, 0.02916632660997443, 0.09212248703639002, 7.45231360132705e-06, 0.2140082858090768, 0.009508570249567472, 0.5162459275326868, 0.001293919095115566, 0.8726414064830788, 0.0001302201041918639, 0.003094500709258363, 0.002116963683292442, 0.001652532423559578, 2.885330472177516e-05, 0.8679630109050446, 0.06064786452319544, 0.01926710656265205, 0.003438784053820811, 0.04592043108186669, 0.009356125116963642, 1.39030344053496e-06, 0.1492915058063837, 0.07707061704057379, 0.07475315743864808, 0.000302419021163877, 0.144336435993247, 0.003223470679335452, 0.03037745915910377, 0.0003011350589031628, 0.006808005110601785, 0.0008232735328502056, 0.03833979319278999, 9.698364220287434e-05, 0.004939487216502053, 6.693653877999158e-05, 0.02813691694081084, 9.485847293237623e-06, 9.213850857247055e-06, 0.0653963700817919, 3.36098340810195e-05, 0.3256932672291724, 4.035388925446032e-05, 0.04374256630355731, 0.0001602246750758031, 0.4014805201846622, 7.992404162601145e-05, 0.01019186788933821, 5.157202070064211e-05, 0.01632615592433439, 2.711206299164022e-05, 1.39112911627399e-05, 0.0001144909315662084, 0.0001470176943661007, 0.008065109594132992, 0.0001053551543690356, 0.09762185907634006, 0.2690693395574275, 2.306365194486018e-06, 0.001629982970373876, 0.0005166683932434172, 0.008811904607316576, 0.004707366984528872, 0.0005329112697905272, 0.004709232000043501, 5.309771784866412e-06, 0.02081799460860159, 0.01482206699240225, 0.02247987076174615, 0.03334725806979871, 0.5823700494422802, 0.6236724985801352, 0.0185646271114748, 0.1682321476102055, 0.5117950109841621, 0.02454309603098215, 0.01143016187387928, 0.03611174379314762, 0.001160042508580727, 0.008675955890656782, 0.0006207030249667641, 0.3189329652004703, 0.009022200481586255, 0.00453169826721376, 0.01175652549884987, 0.03798598471232684, 3.415462094795308e-05, 0.02071616557444895, 0.01314271860208286, 0.2919550074913849, 0.01463675769845591, 0.3808264251791824, 0.0005743039294857045, 0.0001968101730522108, 8.98952537201286e-05, 0.07242504371764499, 0.0003645543853153564, 0.3778182412645538, 6.623577458551056e-06, 0.423433584889663, 6.299717466720515e-06, 0.0002383566395190999, 0.05603244198717539, 0.001549983450584894, 0.002286903228642564, 0.05910553215170956, 0.1696354264894034, 0.008408717444453151, 0.1784153043909985, 0.005750339228228735, 0.1911339411346325, 2.211643409474936e-06, 0.0005399645955134869, 0.0003799502425700674, 0.004668756602094451, 2.190685351762358e-07, 5.683025969646086e-07, 0.01323453573875461],
4 [0.6320870943734679, 0.5484712730611401, 0.5492257737792517, 0.7952445720795884, 0.8651083577332821, 0.5012607949278384, 0.06144835316060489, 0.8953478489268649, 0.623511170207127, 0.3670783290548096, 0.143715002584682, 0.7928204662593729, 0.4832974011618938, 0.5108274907294891, 0.8496550739855554, 0.1893133517110343, 0.1160904368949082, 0.3041937538859427, 0.09444324951555778, 0.09278630856972603, 0.147799788069098, 0.0426634152212833, 0.8785420602235626, 0.4026216782174114, 0.3120378375465396, 0.6543826771662207, 0.8699751769230144, 0.5405380877449835, 0.8693138487984133, 0.686482305253213, 0.7995530565164707, 0.392507997890833, 0.2231942180522403, 0.9333257970032062, 0.1612696179503383, 0.1277791995684988, 0.7777433918064461, 0.5463572711587603, 0.5480962010042225, 0.8902638199188652, 0.8669735693752803, 0.7974305061187666, 0.2449833880092592, 0.9026667690426456, 0.1731651572496988, 0.7766066974692208, 0.8144687030467177, 0.6829640865396805, 0.8729487308364554, 0.8537005360465642, 0.3627933728109908, 0.1555038175261705, 0.6583450331245952, 0.8788374394531219, 0.2142062666186621, 0.6801217034144075, 0.148980651912056, 0.8325752695995462, 0.9024635868351975, 0.7859709097834526, 0.8440126658980578, 0.9055485087777924, 0.7266604429496804, 0.9142663134448874, 0.4138236193712395, 0.01681188022163363, 0.63100018260094, 0.1055161286723332, 0.383439352662872, 0.1982222543750108, 0.2122380372744654, 0.9088833716402204, 0.5579704535685104, 0.07824287873247676, 0.7765279882064482, 0.7682749018879583, 0.4824398541301007, 0.5656352949297849, 0.1273184754304406, 0.3460012685362001, 0.7456605486078066, 0.5233273460187057, 0.4574834694119095, 0.1096418113243125, 0.1319979986864812, 0.9152866949614997, 0.8292917896413513, 0.7234146246969066, 0.9186033593958274, 0.7743249492775025, 0.04770954600992579, 0.8340198218291699, 0.8800999147500712, 0.9021103340009859, 0.3266964459030328, 0.8387973035647739, 0.6458004434313497, 0.8995157766345938, 0.3164866933478583, 0.7779428013707937, 0.4139291394074732, 0.9153718986576534, 0.166535167606684, 0.8044666187136424, 0.1325915468633664, 0.8978671136076242, 0.07979180288034458, 0.06046114687905377, 0.9011813959740612, 0.2949241689393901, 0.6637437560093771, 0.120407670240963, 0.918270154770137, 0.1612696179503383, 0.5953658535509754, 0.2602728295882192, 0.8702215267891145, 0.1267412652275653, 0.9014532903300455, 0.1525180785015703, 0.08833001653827227, 0.2848167216177988, 0.291155693583513, 0.8113681846357962, 0.2481831128877511, 0.8724664599391461, 0.7202683204806987, 0.05345993729671442, 0.5885975575268036, 0.4071786982046535, 0.9237010870137025, 0.6789996143902787, 0.3971013733694621, 0.6667869392290988, 0.07200982497834454, 0.835758859195466, 0.7643535130458815, 0.8644922226864726, 0.9257535746390509, 0.4162981896072208, 0.3748449940749795, 0.9201241749978445, 0.8204110478144335, 0.4862321306527319, 0.8939053225933403, 0.9413039841031908, 0.9238276408307763, 0.3811901386042497, 0.8413935258971738, 0.3846554177087071, 0.6786566853222139, 0.7659643097311739, 0.6629073556777441, 0.7719799010732383, 0.8456463280149575, 0.1642572024254464, 0.8548564514878499, 0.8291552737793674, 0.7053785201185664, 0.932408896468953, 0.6175601494775651, 0.4370814543380974, 0.1790429662743835, 0.256801155005565, 0.8996095443144376, 0.5810041299939207, 0.6191792524328547, 0.04387294749997344, 0.5744116794134839, 0.07008831029467927, 0.3754614887720323, 0.8919015678285099, 0.5872033478817522, 0.720505147827899, 0.9169498862392255, 0.818556681647986, 0.8238276917578375, 0.8149370690440446, 0.8715230063041174, 0.8015022176076705, 0.03940049883343797, 0.6138952750391458, 0.313875602812957, 0.6646831198439501, 0.01708980265774814, 0.02377222152471277, 0.8539739651764133],
5 [0.1441815219614553, 0.3811788719614302, 0.3793237715739675, 0.04185079837763855, 0.04793149737039484, 0.001434248896899514, 1.49523098082053e-05, 0.0277008167876063, 0.3744914560045107, 0.6319307870801458, 0.8562690237525564, 0.2055403603530213, 0.5160299052372981, 0.4885788831746422, 0.1381616154546461, 0.8106184648698082, 0.8838785092265937, 0.6954212180855606, 0.9055396829878539, 0.9071941442535907, 0.8521426405360402, 0.9573360300090934, 0.01875647905621522, 0.5968721987872823, 0.6876908033558112, 0.3349067753246693, 0.1194348350229463, 0.4576372047986426, 0.02665512710380765, 0.3061230147901675, 0.1849612363201747, 0.6066360112966892, 0.7766155478193099, 0.02288288391704356, 0.8385701573745858, 3.417968240597176e-05, 0.2148658758657946, 0.3868937587521149, 0.3821775534954441, 0.01571243596007, 0.02251556487877614, 0.1892829931254875, 0.7545509987757878, 0.07222771098010485, 0.8268075811870527, 0.004611759841360215, 0.1791438741625844, 0.3095956918206536, 0.07461829037112036, 0.01729679538595195, 0.0009599289499872507, 0.0001298416501157798, 0.340808592054677, 0.04794915019190218, 0.0002873798909779559, 0.004805668908448148, 0.0001704336727469521, 0.1398554475278166, 0.08454318381027025, 0.1978723238218864, 0.01780013211028798, 0.02864790102182029, 0.2653909498810832, 0.04949975452158001, 0.58504926155725, 0.9831878687195582, 0.3678010821193476, 0.8944688810407423, 0.6158229644492531, 0.8016338126741221, 0.7873997050245573, 0.06195030174980526, 0.3499070593950995, 0.921749668953922, 0.009463725984474914, 0.2222165278624742, 0.001314218337212393, 0.4330707859750995, 4.011808648077104e-05, 0.6538685113596081, 0.2512449506829349, 0.4745556902980019, 0.5408639981645308, 0.8903293353709656, 3.899040847425775e-05, 0.0240654405153047, 0.1514411037959966, 0.2731465912492725, 0.03547620952230578, 0.2163189256055338, 0.9522890636866338, 0.01668867236444656, 0.04282946820935509, 0.02313650856036603, 0.6730011350758033, 0.01686626044197891, 0.3509760858893148, 0.07010676420630228, 0.6832121715932385, 0.2152491935186044, 0.5852475870596766, 0.04628830814955653, 0.833367848751113, 0.1905938940698556, 0.8673415165978536, 0.07399596945156511, 0.9201987112723621, 0.9395296392700889, 0.03342223394414681, 0.7050422212265288, 0.01056297676145055, 0.8795519758697826, 0.03798727892630575, 0.8385701573745858, 0.003153626264362388, 0.7396472463701548, 0.1195866053215473, 0.873207162751734, 0.08222055374562, 0.8474548094354379, 0.911656072170565, 0.715068787450635, 0.7086972887221209, 0.1805667057700708, 0.7517115319578799, 0.02991168098451388, 0.01066233996187374, 0.9465377563380911, 0.4097724595028225, 0.5923046334021032, 0.06748700837898086, 0.3162930186251925, 0.6023657153607472, 0.3285038287708577, 0.9279848652498707, 0.1434231461959324, 0.2208244199617161, 0.1130279065517811, 0.04089916729115029, 0.001331760950498852, 0.001482507344885308, 0.06131119789068074, 0.01135680457536089, 0.001972858363106022, 0.08155158137567768, 0.04726585402292987, 0.04006061537607595, 0.6176498188871696, 0.1499305182121694, 0.6147238792663262, 0.002410349477315677, 0.2250134897872399, 0.3325609460550422, 0.2162635734279119, 0.1163676872727156, 0.8357086429536057, 0.1244273829377012, 0.1577020076185499, 0.002666472390048749, 0.05295434583259118, 0.001613425343252465, 0.5623442417324168, 0.8207602235525642, 0.743108949740715, 0.02796541196791737, 0.4186313156207639, 0.003002506302591648, 0.956120428922568, 0.002154735696853137, 0.929905389987854, 0.6243001545884486, 0.05206599018431463, 0.4112466686676627, 0.2772079489434584, 0.02394458160906492, 0.01180789186261077, 0.1677635907977094, 0.006647626564956893, 0.1227266544676539, 0.007363841257697064, 0.9605972895231527, 0.3855647603653409, 0.6857444469444728, 0.3306481235539554, 0.9829099782737166, 0.9762272101726904, 0.1327914990848322]
6 ],
7 "analysis":{
8 "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
9 "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353. v2.2 adds support for multiple-hit models. v2.3 adds support for SRV",
10 "contact":"spond@temple.edu",
11 "info":"aBSREL (Adaptive branch-site random effects likelihood)\n uses an adaptive random effects branch-site model framework\n to test whether each branch has evolved under positive selection,\n using a procedure which infers an optimal number of rate categories per branch.",
12 "requirements":"in-frame codon alignment and a phylogenetic tree",
13 "version":"2.3"
14 },
15 "branch attributes":{
16 "0":{
17 "Baboon":{
18 "Baseline MG94xREV":0.001882994109917251,
19 "Baseline MG94xREV omega ratio":0,
20 "Corrected P-value":1,
21 "Full adaptive model":0.001888788495524889,
22 "Full adaptive model (non-synonymous subs/site)":1e-10,
23 "Full adaptive model (synonymous subs/site)":0.001888788495524889,
24 "LRT":0,
25 "Nucleotide GTR":0.001685167654714891,
26 "Rate Distributions": [
27 [0, 1]
28 ],
29 "Rate classes":1,
30 "Uncorrected P-value":1,
31 "original name":"Baboon",
32 "rate at which 2 nucleotides are changed instantly within a single codon":0
33 },
34 "Cat":{
35 "Baseline MG94xREV":0.2956038491638456,
36 "Baseline MG94xREV omega ratio":1.387276691142692,
37 "Corrected P-value":1,
38 "Full adaptive model":0.2987657142024844,
39 "Full adaptive model (non-synonymous subs/site)":0.2433925676712428,
40 "Full adaptive model (synonymous subs/site)":0.05537314653124186,
41 "LRT":0.8385257143854687,
42 "Nucleotide GTR":0.2660536011315811,
43 "Rate Distributions": [
44 [1.406509052931997, 1]
45 ],
46 "Rate classes":1,
47 "Uncorrected P-value":0.2692231522977311,
48 "original name":"Cat",
49 "rate at which 2 nucleotides are changed instantly within a single codon":0.2039176940606485
50 },
51 "Chimp":{
52 "Baseline MG94xREV":0.001849682046955941,
53 "Baseline MG94xREV omega ratio":10000000000,
54 "Corrected P-value":1,
55 "Full adaptive model":0.001852710195778403,
56 "Full adaptive model (non-synonymous subs/site)":0.001852710195778403,
57 "Full adaptive model (synonymous subs/site)":1e-10,
58 "LRT":0.6095489899789754,
59 "Nucleotide GTR":0.001820258053351119,
60 "Rate Distributions": [
61 [10000000000, 1]
62 ],
63 "Rate classes":1,
64 "Uncorrected P-value":0.3081784202350423,
65 "original name":"Chimp",
66 "rate at which 2 nucleotides are changed instantly within a single codon":0
67 },
68 "Cow":{
69 "Baseline MG94xREV":0.2725380828787176,
70 "Baseline MG94xREV omega ratio":1.996288552263199,
71 "Corrected P-value":1,
72 "Full adaptive model":0.2767543531983568,
73 "Full adaptive model (non-synonymous subs/site)":0.2381665266426745,
74 "Full adaptive model (synonymous subs/site)":0.03858782655568219,
75 "LRT":3.11056227267909,
76 "Nucleotide GTR":0.2480198736772598,
77 "Rate Distributions": [
78 [2.042233367641365, 1]
79 ],
80 "Rate classes":1,
81 "Uncorrected P-value":0.07889622593515888,
82 "original name":"Cow",
83 "rate at which 2 nucleotides are changed instantly within a single codon":0.1380461206420348
84 },
85 "Horse":{
86 "Baseline MG94xREV":0.2306806115249962,
87 "Baseline MG94xREV omega ratio":1.164040491954013,
88 "Corrected P-value":1,
89 "Full adaptive model":0.2320795562671627,
90 "Full adaptive model (non-synonymous subs/site)":0.1780556222700155,
91 "Full adaptive model (synonymous subs/site)":0.05402393399714727,
92 "LRT":0.2293786685804662,
93 "Nucleotide GTR":0.2090998951755368,
94 "Rate Distributions": [
95 [1.174701177865617, 1]
96 ],
97 "Rate classes":1,
98 "Uncorrected P-value":0.393889915055757,
99 "original name":"Horse",
100 "rate at which 2 nucleotides are changed instantly within a single codon":0
101 },
102 "Human":{
103 "Baseline MG94xREV":0,
104 "Baseline MG94xREV omega ratio":1,
105 "Corrected P-value":1,
106 "Full adaptive model":0,
107 "Full adaptive model (non-synonymous subs/site)":1e-10,
108 "Full adaptive model (synonymous subs/site)":1e-10,
109 "LRT":0,
110 "Nucleotide GTR":0,
111 "Rate Distributions": [
112 [1, 1]
113 ],
114 "Rate classes":1,
115 "Uncorrected P-value":1,
116 "original name":"Human",
117 "rate at which 2 nucleotides are changed instantly within a single codon":0.0009494209875164728
118 },
119 "Mouse":{
120 "Baseline MG94xREV":0.130389131191465,
121 "Baseline MG94xREV omega ratio":0.5075430486034895,
122 "Corrected P-value":1,
123 "Full adaptive model":0.1314019024803463,
124 "Full adaptive model (non-synonymous subs/site)":0.07806862630983659,
125 "Full adaptive model (synonymous subs/site)":0.05333327617050967,
126 "LRT":0,
127 "Nucleotide GTR":0.1181058300538561,
128 "Rate Distributions": [
129 [0.5153237391744061, 1]
130 ],
131 "Rate classes":1,
132 "Uncorrected P-value":1,
133 "original name":"Mouse",
134 "rate at which 2 nucleotides are changed instantly within a single codon":0.02214869577417109
135 },
136 "Node1":{
137 "Baseline MG94xREV":0.3335904378274563,
138 "Baseline MG94xREV omega ratio":0.296025779706705,
139 "Corrected P-value":1,
140 "Full adaptive model":0.3367504162367471,
141 "Full adaptive model (non-synonymous subs/site)":0.1724145968502319,
142 "Full adaptive model (synonymous subs/site)":0.1643358193865155,
143 "LRT":0,
144 "Nucleotide GTR":0.2767105173979571,
145 "Rate Distributions": [
146 [0.3015051917009056, 1]
147 ],
148 "Rate classes":1,
149 "Uncorrected P-value":1,
150 "rate at which 2 nucleotides are changed instantly within a single codon":0.4322434210228028
151 },
152 "Node12":{
153 "Baseline MG94xREV":0.01392429623408649,
154 "Baseline MG94xREV omega ratio":0.2780699887855826,
155 "Corrected P-value":1,
156 "Full adaptive model":0.01389906280188583,
157 "Full adaptive model (non-synonymous subs/site)":0.006925004412300655,
158 "Full adaptive model (synonymous subs/site)":0.006974058389585205,
159 "LRT":0,
160 "Nucleotide GTR":0.01784222107494562,
161 "Rate Distributions": [
162 [0.2813759516294281, 1]
163 ],
164 "Rate classes":1,
165 "Uncorrected P-value":1,
166 "rate at which 2 nucleotides are changed instantly within a single codon":0.4640974620285408
167 },
168 "Node2":{
169 "Baseline MG94xREV":0.04571805957848055,
170 "Baseline MG94xREV omega ratio":0.07808093503260165,
171 "Corrected P-value":1,
172 "Full adaptive model":0.0459318071864371,
173 "Full adaptive model (non-synonymous subs/site)":0.02632650948831447,
174 "Full adaptive model (synonymous subs/site)":0.01960529769812262,
175 "LRT":0,
176 "Nucleotide GTR":0.06614755778044307,
177 "Rate Distributions": [
178 [0.07994399997950775, 1]
179 ],
180 "Rate classes":1,
181 "Uncorrected P-value":1,
182 "rate at which 2 nucleotides are changed instantly within a single codon":10.77888358494443
183 },
184 "Node3":{
185 "Baseline MG94xREV":0.1076878090259787,
186 "Baseline MG94xREV omega ratio":1.418168092305362,
187 "Corrected P-value":1,
188 "Full adaptive model":0.1082923487440297,
189 "Full adaptive model (non-synonymous subs/site)":0.08948990966777266,
190 "Full adaptive model (synonymous subs/site)":0.01880243907625684,
191 "LRT":0.2456529644996408,
192 "Nucleotide GTR":0.09883748387954429,
193 "Rate Distributions": [
194 [1.433858907010162, 1]
195 ],
196 "Rate classes":1,
197 "Uncorrected P-value":0.389355679288724,
198 "rate at which 2 nucleotides are changed instantly within a single codon":0.3287265444712935
199 },
200 "Node8":{
201 "Baseline MG94xREV":0.1135770124969486,
202 "Baseline MG94xREV omega ratio":2.028136557891868,
203 "Corrected P-value":1,
204 "Full adaptive model":0.1147398059647541,
205 "Full adaptive model (non-synonymous subs/site)":0.0990475665351926,
206 "Full adaptive model (synonymous subs/site)":0.01569223942956148,
207 "LRT":0.7886998749927443,
208 "Nucleotide GTR":0.1062201244057951,
209 "Rate Distributions": [
210 [1.988476719481082, 1]
211 ],
212 "Rate classes":1,
213 "Uncorrected P-value":0.2771341436242022,
214 "rate at which 2 nucleotides are changed instantly within a single codon":0.2354207827705045
215 },
216 "Node9":{
217 "Baseline MG94xREV":0.03003888198106763,
218 "Baseline MG94xREV omega ratio":0.4077675922423373,
219 "Corrected P-value":1,
220 "Full adaptive model":0.03019973043687331,
221 "Full adaptive model (non-synonymous subs/site)":0.01619043357790366,
222 "Full adaptive model (synonymous subs/site)":0.01400929685896962,
223 "LRT":0,
224 "Nucleotide GTR":0.02567813733543303,
225 "Rate Distributions": [
226 [0.4119078417573153, 1]
227 ],
228 "Rate classes":1,
229 "Uncorrected P-value":1,
230 "rate at which 2 nucleotides are changed instantly within a single codon":0
231 },
232 "Pig":{
233 "Baseline MG94xREV":0.217114312357174,
234 "Baseline MG94xREV omega ratio":1.283370430439691,
235 "Corrected P-value":1,
236 "Full adaptive model":0.2181331361104026,
237 "Full adaptive model (non-synonymous subs/site)":0.1712686263446052,
238 "Full adaptive model (synonymous subs/site)":0.04686450976579729,
239 "LRT":0.5406119303397645,
240 "Nucleotide GTR":0.1871390433004313,
241 "Rate Distributions": [
242 [1.302541757406645, 1]
243 ],
244 "Rate classes":1,
245 "Uncorrected P-value":0.3213796354214938,
246 "original name":"Pig",
247 "rate at which 2 nucleotides are changed instantly within a single codon":0
248 },
249 "Rat":{
250 "Baseline MG94xREV":0.06785652890791004,
251 "Baseline MG94xREV omega ratio":0.9234518387715737,
252 "Corrected P-value":1,
253 "Full adaptive model":0.06783877994658692,
254 "Full adaptive model (non-synonymous subs/site)":0.04934287026354431,
255 "Full adaptive model (synonymous subs/site)":0.01849590968304254,
256 "LRT":0,
257 "Nucleotide GTR":0.06661490534189227,
258 "Rate Distributions": [
259 [0.939079296251313, 1]
260 ],
261 "Rate classes":1,
262 "Uncorrected P-value":1,
263 "original name":"Rat",
264 "rate at which 2 nucleotides are changed instantly within a single codon":0.02234985038534893
265 },
266 "RhMonkey":{
267 "Baseline MG94xREV":0.0036869629402653,
268 "Baseline MG94xREV omega ratio":10000000000,
269 "Corrected P-value":1,
270 "Full adaptive model":0.003691831254195047,
271 "Full adaptive model (non-synonymous subs/site)":0.003691831254195047,
272 "Full adaptive model (synonymous subs/site)":1e-10,
273 "LRT":1.049935795353122,
274 "Nucleotide GTR":0.003778804730491441,
275 "Rate Distributions": [
276 [10000000000, 1]
277 ],
278 "Rate classes":1,
279 "Uncorrected P-value":0.2385766813428075,
280 "original name":"RhMonkey",
281 "rate at which 2 nucleotides are changed instantly within a single codon":0
282 }
283 },
284 "attributes":{
285 "Baseline MG94xREV":{
286 "attribute type":"branch length",
287 "display order":1
288 },
289 "Baseline MG94xREV omega ratio":{
290 "attribute type":"branch label",
291 "display order":1
292 },
293 "Corrected P-value":{
294 "attribute type":"branch label",
295 "display order":6
296 },
297 "Full adaptive model":{
298 "attribute type":"branch length",
299 "display order":2
300 },
301 "Full adaptive model (non-synonymous subs/site)":{
302 "attribute type":"branch label",
303 "display order":10
304 },
305 "Full adaptive model (synonymous subs/site)":{
306 "attribute type":"branch label",
307 "display order":9
308 },
309 "LRT":{
310 "attribute type":"branch label",
311 "display order":4
312 },
313 "Nucleotide GTR":{
314 "attribute type":"branch length",
315 "display order":0
316 },
317 "Rate Distributions":{
318 "attribute type":"branch label",
319 "display order":3
320 },
321 "Rate classes":{
322 "attribute type":"branch label",
323 "display order":2
324 },
325 "Uncorrected P-value":{
326 "attribute type":"branch label",
327 "display order":5
328 },
329 "original name":{
330 "attribute type":"node label",
331 "display order":-1
332 },
333 "rate at which 2 nucleotides are changed instantly within a single codon":{
334 "attribute type":"branch label",
335 "display order":7
336 }
337 }
338 },
339 "data partitions":{
340 "0":{
341 "coverage": [
342 [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]
343 ],
344 "name":"absrel.filter.default"
345 }
346 },
347 "fits":{
348 "Baseline MG94xREV":{
349 "AIC-c":6938.369899478594,
350 "Equilibrium frequencies": [
351 [0.04876086397632926],
352 [0.03982224127745371],
353 [0.0494959405650269],
354 [0.04152830682371345],
355 [0.01810345074594235],
356 [0.01478480742075003],
357 [0.01837636270304883],
358 [0.01541821854326533],
359 [0.01892910005547028],
360 [0.01545910240515689],
361 [0.01921445878706794],
362 [0.01612140169177368],
363 [0.02829747763884322],
364 [0.02311011106415996],
365 [0.02872406592369408],
366 [0.02410019507229243],
367 [0.01663805943190806],
368 [0.01358804506433061],
369 [0.01688888041768248],
370 [0.01417018446135155],
371 [0.006177213955434187],
372 [0.005044834822351987],
373 [0.006270336287397383],
374 [0.00526096577332031],
375 [0.006458939937330408],
376 [0.005274916061901906],
377 [0.006556309326397028],
378 [0.005500904159606446],
379 [0.009655594186286731],
380 [0.007885574003572761],
381 [0.009801153568494354],
382 [0.008223407979974132],
383 [0.03327785448210915],
384 [0.02717750758119989],
385 [0.03377952261833742],
386 [0.02834184710178207],
387 [0.01235507229404208],
388 [0.01009019590244688],
389 [0.01254132667213156],
390 [0.01052248035033209],
391 [0.01291855364640413],
392 [0.01055038238273567],
393 [0.01311330258173711],
394 [0.01100238215235291],
395 [0.01931219560697892],
396 [0.0157719705998612],
397 [0.01960332955558842],
398 [0.01644767379420349],
399 [0.01965132601881859],
400 [0.02049322866376102],
401 [0.008933621043463411],
402 [0.007295949736387736],
403 [0.009068296583349953],
404 [0.007608523013862737],
405 [0.007628698224327205],
406 [0.009481877006094248],
407 [0.00795552712159237],
408 [0.01396413011303752],
409 [0.01140428846505027],
410 [0.01417464125436193],
411 [0.01189287130232129]
412 ],
413 "Log Likelihood":-3399.656647852504,
414 "Rate Distributions":{
415 "Per-branch delta":{
416 "2.5%":0,
417 "97.5%":10.66318587577853,
418 "Mean":1.142287895998736,
419 "Median":0.2080459069952131
420 },
421 "Per-branch omega":{
422 "2.5%":0,
423 "97.5%":2.028136557891868,
424 "Mean":666666667.5178814,
425 "Median":1
426 },
427 "Synonymous site-to-site rates":{
428 "0":{
429 "proportion":0.3499070593950995,
430 "rate":0.3584907731592092
431 },
432 "1":{
433 "proportion":0.5579704535685105,
434 "rate":1.083607309819905
435 },
436 "2":{
437 "proportion":0.09212248703639001,
438 "rate":2.93023662601063
439 }
440 }
441 },
442 "display order":1,
443 "estimated parameters":67
444 },
445 "Full adaptive model":{
446 "AIC-c":6937.867430345418,
447 "Log Likelihood":-3399.405413285916,
448 "Rate Distributions":{
449 },
450 "display order":2,
451 "estimated parameters":67
452 },
453 "Nucleotide GTR":{
454 "AIC-c":7112.857288723968,
455 "Equilibrium frequencies": [
456 [0.3592490842490842],
457 [0.181959706959707],
458 [0.240018315018315],
459 [0.2187728937728937]
460 ],
461 "Log Likelihood":-3532.321213744258,
462 "Rate Distributions":{
463 "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,
464 "Substitution rate from nucleotide A to nucleotide G":1,
465 "Substitution rate from nucleotide A to nucleotide T":0.2646800222727828,
466 "Substitution rate from nucleotide C to nucleotide G":0.4918071762416347,
467 "Substitution rate from nucleotide C to nucleotide T":1.028675134787727,
468 "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741
469 },
470 "display order":0,
471 "estimated parameters":24
472 }
473 },
474 "input":{
475 "file name":"/tmp/tmpasswxnks/job_working_directory/000/9/working/./input.fasta",
476 "number of sequences":10,
477 "number of sites":187,
478 "partition count":1,
479 "trees":{
480 "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)"
481 }
482 },
483 "runtime":"2.5.36",
484 "test results":{
485 "P-value threshold":0.05,
486 "positive test results":0,
487 "tested":16
488 },
489 "tested":{
490 "0":{
491 "Baboon":"test",
492 "Cat":"test",
493 "Chimp":"test",
494 "Cow":"test",
495 "Horse":"test",
496 "Human":"test",
497 "Mouse":"test",
498 "Node1":"test",
499 "Node12":"test",
500 "Node2":"test",
501 "Node3":"test",
502 "Node8":"test",
503 "Node9":"test",
504 "Pig":"test",
505 "Rat":"test",
506 "RhMonkey":"test"
507 }
508 },
509 "timers":{
510 "Baseline model fitting":{
511 "order":2,
512 "timer":129
513 },
514 "Complexity analysis":{
515 "order":3,
516 "timer":406
517 },
518 "Full adaptive model fitting":{
519 "order":4,
520 "timer":46
521 },
522 "Overall":{
523 "order":0,
524 "timer":1006
525 },
526 "Preliminary model fitting":{
527 "order":1,
528 "timer":0
529 },
530 "Testing for selection":{
531 "order":5,
532 "timer":424
533 }
534 }
535 }