comparison test-data/busted-out1.json @ 0:ae7c42d49717 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
author iuc
date Wed, 21 Aug 2019 12:25:55 -0400
parents
children d2acd8d86e55
comparison
equal deleted inserted replaced
-1:000000000000 0:ae7c42d49717
1 {
2 "analysis":{
3 "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted jointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. Assuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio style analysis to explore which individual sites may have been subject to selection.",
4 "version":"1.2",
5 "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
6 "authors":"Sergei L Kosakovsky Pond",
7 "contact":"spond@temple.edu",
8 "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})"
9 },
10 "input":{
11 "file name":"/Users/stephenshank/Documents/Galaxy/tools-iuc/tools/hyphy/test-data/absrel-in1.fa",
12 "number of sequences":10,
13 "number of sites":187,
14 "partition count":1,
15 "trees":{
16 "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)"
17 }
18 },
19 "background":0,
20 "fits":{
21 "Nucleotide GTR":{
22 "Log Likelihood":-3531.963798530155,
23 "estimated parameters":24,
24 "AIC-c":7112.142458295762,
25 "Equilibrium frequencies":[
26 [0.3563279857397504],
27 [0.1837789661319073],
28 [0.2402852049910873],
29 [0.2196078431372549]
30 ],
31 "Rate Distributions":{
32 "Substitution rate from nucleotide A to nucleotide C":0.5474490057204714,
33 "Substitution rate from nucleotide A to nucleotide G":1,
34 "Substitution rate from nucleotide A to nucleotide T":0.2645352969683238,
35 "Substitution rate from nucleotide C to nucleotide G":0.4863078374555331,
36 "Substitution rate from nucleotide C to nucleotide T":1.018028772244997,
37 "Substitution rate from nucleotide G to nucleotide T":0.3025951149895378
38 },
39 "display order":0
40 },
41 "MG94xREV with separate rates for branch sets":{
42 "Log Likelihood":-3466.725508616141,
43 "estimated parameters":31,
44 "AIC-c":6996.530451399855,
45 "Equilibrium frequencies":[
46 [0.04785168648208005],
47 [0.03911346079312019],
48 [0.04842054060317301],
49 [0.04069665666515385],
50 [0.01817010744778396],
51 [0.01485205303123071],
52 [0.01838611113045968],
53 [0.01545321970309948],
54 [0.0190138898893362],
55 [0.01554175184587827],
56 [0.01923992433904378],
57 [0.01617083546230154],
58 [0.02796925133965702],
59 [0.02286176927319543],
60 [0.02830174586718859],
61 [0.02378714529482007],
62 [0.01687870337957799],
63 [0.01379647304851128],
64 [0.01707935503225849],
65 [0.01435491300079667],
66 [0.006409133648843443],
67 [0.005238757839512795],
68 [0.006485324528555602],
69 [0.005450807083377185],
70 [0.006706760641638982],
71 [0.005482034985409045],
72 [0.006786489669196017],
73 [0.005703931360295163],
74 [0.009865581170012171],
75 [0.008064021368173151],
76 [0.009982861811889655],
77 [0.008390428826966174],
78 [0.03287895020631181],
79 [0.02687490503171972],
80 [0.033269810543681],
81 [0.0279627207822247],
82 [0.01248470225271473],
83 [0.01020486315060615],
84 [0.01263311863778268],
85 [0.01061792547971484],
86 [0.01306446616325414],
87 [0.01067875601941112],
88 [0.01321977470017749],
89 [0.01111100011404158],
90 [0.01921770557551369],
91 [0.01570834862514353],
92 [0.01944616295744266],
93 [0.01634417558076203],
94 [0.01975257768318274],
95 [0.02055210293142003],
96 [0.009176034326710849],
97 [0.007500393094996483],
98 [0.00928511773266342],
99 [0.007803986567571961],
100 [0.00784869593340758],
101 [0.009716299514778986],
102 [0.008166387662818644],
103 [0.01412467213650941],
104 [0.01154535713247913],
105 [0.01429258425298098],
106 [0.01201267864744234]
107 ],
108 "Rate Distributions":{
109 "non-synonymous/synonymous rate ratio for *test*":[
110 [0.9970623081401093, 1]
111 ]
112 },
113 "display order":1
114 },
115 "Unconstrained model":{
116 "Log Likelihood":-3437.188861487313,
117 "estimated parameters":35,
118 "AIC-c":6945.751768776152,
119 "Rate Distributions":{
120 "Test":{
121 "0":{
122 "omega":0.1052869846173941,
123 "proportion":0.2379046712842726
124 },
125 "1":{
126 "omega":0.2107329369900513,
127 "proportion":0.4121351840538361
128 },
129 "2":{
130 "omega":3.951290720456698,
131 "proportion":0.3499601446618912
132 }
133 }
134 },
135 "display order":2
136 },
137 "Constrained model":{
138 "Log Likelihood":-3459.576322342121,
139 "estimated parameters":34,
140 "AIC-c":6988.449647409037,
141 "Rate Distributions":{
142 "Test":{
143 "0":{
144 "omega":0,
145 "proportion":0.1368169359858254
146 },
147 "1":{
148 "omega":0,
149 "proportion":0.09947859848803366
150 },
151 "2":{
152 "omega":1,
153 "proportion":0.7637044655261409
154 }
155 }
156 },
157 "display order":3
158 }
159 },
160 "timers":{
161 "Overall":{
162 "timer":79,
163 "order":0
164 },
165 "Preliminary model fitting":{
166 "timer":22,
167 "order":1
168 },
169 "Unconstrained BUSTED model fitting":{
170 "timer":29,
171 "order":2
172 },
173 "Constrained BUSTED model fitting":{
174 "timer":18,
175 "order":3
176 }
177 },
178 "Site Log Likelihood":{
179 "unconstrained":[
180 [-9.761780003252589, -3.556981916965661, -3.871692954311539, -17.99295796244379, -17.6956827873063, -30.01736049845984, -32.80456708119989, -24.24615674389706, -17.22716501528761, -10.63078274532717, -17.5513791952437, -23.10676596882748, -20.1589722777239, -16.08007905666529, -22.07489132346995, -13.27698585999586, -11.57373969856821, -15.0218610811265, -12.31301984930962, -9.878172230255872, -9.283873417740052, -12.8230707251624, -24.29926852464868, -14.11614921655551, -14.80291769006257, -14.24359374301642, -21.23808978297999, -15.20669497937926, -21.11914571105627, -18.695897789747, -22.4289474056158, -14.71510620919697, -10.95989097579746, -28.25520114439835, -7.114758548777005, -35.1823654002276, -15.94120703275923, -4.330001696693314, -4.810804241726376, -24.36449596493429, -19.85422544995369, -20.21977077882305, -12.00277035613209, -19.6600724196642, -15.22159826235479, -24.22386090964918, -16.83876198375444, -15.39919245352698, -20.55491461157309, -23.30374279272433, -29.43636445622652, -31.41899626907746, -20.08375283223842, -21.69892250748334, -31.28859827841539, -26.08296126442238, -28.95584777914672, -20.97050845715194, -22.87836756552637, -16.10418205553547, -21.63783799404863, -22.29130394316017, -18.35819291264508, -23.0059705707678, -14.03484863809933, -9.416359563812415, -18.79111063130158, -12.78164205666208, -11.19294341786628, -10.24271903306927, -9.811969009737055, -20.99099337931294, -5.038213419512006, -12.36951590374203, -23.75822209792559, -24.38317903225788, -29.79314521637115, -15.03360351335341, -30.15269907145897, -15.40303952466706, -22.87293615165179, -10.81368963977958, -12.47042186757648, -11.73824102802078, -34.62663852693693, -22.96333978037858, -16.64020476652507, -18.34587549890907, -24.44431984136763, -15.73196577376136, -10.85174956948496, -20.76376393713096, -22.87186260864842, -24.188197096568, -13.78231255943875, -23.02551088711758, -13.64118597104227, -23.70873447722415, -13.43680638220221, -18.36670985939329, -14.24443250362629, -20.74306008601751, -11.19634482669214, -20.60160418194348, -11.398502668876, -23.3132179060432, -12.41458242767006, -8.59839648909502, -21.13421524691898, -18.70680195104232, -24.04441379518424, -9.992102259489076, -22.86252385976109, -7.114758548777005, -27.5565726745568, -12.87223741705519, -24.48854177549546, -9.791375505313344, -21.57931931289719, -13.73761157881194, -12.7003636235767, -15.92686724109126, -13.25111195536186, -19.5598880256505, -12.78420433838847, -25.3479232600814, -23.21813833324584, -11.87082416732899, -18.34124875195977, -13.39208375265505, -23.22887768380001, -13.67243009919361, -12.64371510970045, -15.23267340039615, -12.46602644865305, -15.78570032614895, -20.49430844113086, -16.74759955468868, -21.37629168953962, -31.91852172562975, -32.91408279059539, -28.11259733944721, -23.28467231775043, -25.08348256456863, -24.36722240264622, -27.85361506098191, -22.81200431380501, -12.06099437357067, -21.72512567277257, -14.75966862326406, -26.55673909887922, -15.9891326482062, -16.67305867563187, -15.89127092598368, -17.11654012165223, -15.14718002836891, -19.22179155508141, -20.14784462411578, -27.16144224004015, -22.80088235078308, -29.6346258900827, -14.87414990449581, -10.09001804965354, -14.06722825110506, -21.55226091029841, -17.89237433412178, -26.9887399484436, -7.247032599266484, -29.10107988545393, -11.92987823423617, -14.41471074589252, -20.22815853097579, -13.94727875575511, -24.40018676619344, -24.57667974105677, -29.23515533817404, -18.36670890820324, -29.22340700233682, -17.74018014861057, -26.54152667547728, -8.953815058919133, -20.2800904930613, -14.09345734559062, -14.03391364104814, -9.421270195111878, -9.469430414396884, -20.11488196129918]
181 ],
182 "constrained":[
183 [-10.85606152021318, -3.471229863506585, -3.800029997251122, -19.76181202731181, -18.99505347406228, -33.70672014040629, -40.08617973771972, -28.08241530494764, -19.10728836136312, -9.985069679724274, -15.75689438367687, -24.2738510731431, -19.60585366503884, -16.3091575384683, -22.29810643714523, -11.58047190013798, -10.65369978272362, -15.34194795652741, -10.92534862913859, -8.262063009605756, -7.795056828277495, -10.98823292846032, -26.45715781872953, -13.56039498470006, -14.80733027279041, -14.97339798653168, -22.83819293785454, -15.99960324964237, -23.05374383928736, -18.64540846688676, -22.52507508510511, -14.06096141784007, -9.950850202190837, -31.09994454740333, -5.657479911616817, -40.20764738574088, -15.24880713029523, -4.245259501823234, -4.75823140493186, -26.42921606238378, -21.05932496028346, -21.24380652339677, -12.51510927509652, -19.4431274563198, -13.45707855557425, -27.34067162541028, -16.92068505165836, -15.27874830129921, -21.78078086811648, -25.74988026772384, -32.3591534741427, -36.92136999297909, -20.86637747607929, -26.21690123953934, -38.38842669761863, -29.5707349344923, -34.78024872766768, -22.34647319638493, -24.42164357523894, -15.89813120477618, -24.88114938112022, -24.16882658381608, -19.15062432752575, -25.32782323726632, -12.54397568681377, -7.658560467541037, -20.06316291990198, -11.38834848993708, -10.34978442983486, -8.798066094581541, -8.365525022998657, -23.37022898655908, -5.038213419512005, -11.73698294324726, -26.59271763114307, -27.51600374427774, -33.19580365368542, -14.08391822294567, -37.61485496561196, -14.61037124768515, -24.95712121575756, -9.468302677820519, -11.80724915343188, -10.17626631190552, -39.82223560997122, -23.22993675058718, -15.29814440122603, -18.59041764178898, -25.85430435634182, -16.63728997890176, -9.088390872315317, -23.36486681955814, -25.10120831076364, -26.87850226687513, -12.5163839486935, -25.46276168897045, -13.30043078187602, -26.00037628519058, -12.36183639601969, -19.32639068670407, -13.90921600814463, -23.30517706031209, -10.38197265044853, -21.48132876823857, -10.34226801788524, -25.48737661714055, -11.54862505674196, -7.268129324767196, -23.12171070541123, -16.87868227611221, -26.86559749366134, -8.472693915554212, -26.90473561049812, -5.657479911616817, -30.14077517350693, -11.1338558936567, -26.90933331018406, -8.683054657060978, -22.93750465468248, -12.09242051639567, -12.24278260635322, -16.46214458935806, -11.52233069441597, -19.57563980700768, -11.24562305579595, -28.73517189370709, -26.5995022362575, -10.11077097725237, -17.64257519637804, -12.22627059873072, -25.794387889477, -13.00339712214579, -11.44442645621986, -15.23294312487709, -11.01984685521603, -15.23436625095256, -21.84913978769858, -17.43830973910884, -24.04200658810043, -36.02241585126664, -39.74114047148559, -30.51107839063483, -25.24778323303905, -29.10134605686299, -27.4051878646382, -29.40431078055861, -26.00565963206897, -11.37219430365775, -23.62588495555996, -13.84835203928034, -30.39496528205261, -17.46875631982503, -16.48393583594229, -16.95840797360417, -18.18414725855796, -14.60783644912805, -20.36574492127523, -22.08905835390395, -30.09377992258299, -24.20776345765027, -33.87407556904575, -13.85334118326135, -9.038547460214009, -12.31883826587824, -23.76076017501662, -16.13507283064812, -31.74425687978529, -5.621431190076298, -32.77926379309199, -10.93320737320503, -14.18712500350103, -23.00952178187488, -13.74809094768596, -27.13572996742387, -27.80389794085873, -33.12824566268318, -18.82222585779942, -32.59467769783617, -18.82117621115135, -28.87355399347379, -7.202495413751149, -20.10273643846979, -13.55384673130033, -13.92541401636034, -7.622924396558326, -8.028485273604586, -20.99338693632994]
184 ],
185 "optimized null":[
186 [-9.984891074365004, -3.552861592101205, -3.869898855143417, -18.01518487110813, -17.38504309777226, -29.7102253995114, -33.97262688823771, -25.58952900757811, -18.32327569996284, -10.43679078115309, -17.34797699860558, -23.44071853477707, -20.13369389964067, -16.23209205498968, -20.84681207056716, -13.14211233137375, -11.68410006052765, -15.49850331840433, -12.80349920668154, -9.951696917262908, -9.674794006047554, -13.35878598779897, -23.86875827725563, -13.92120845548608, -15.25915378398707, -14.40626012443236, -21.26593666732801, -15.47805189201786, -20.8967440084538, -17.92205772755303, -21.52612599164656, -14.37849206841925, -11.28236683284286, -27.85944578501297, -7.045007615754844, -35.50167243235479, -15.43207104477209, -4.330649700739783, -4.821509537453836, -24.61117309405466, -19.66210749973598, -19.61978108110112, -13.06931658869425, -18.90379736902437, -15.17248506099829, -24.20575482256608, -16.80670782290678, -15.1069403318206, -20.23445804273289, -22.93238636351499, -28.6422792678352, -31.91671871385733, -19.7070935797896, -24.16184701754757, -32.87373578813684, -25.97502236883938, -30.04305670719911, -20.66008132977401, -22.5476319199698, -15.71574496122768, -21.82260087605331, -22.33213004101708, -17.88649192977146, -22.85979453942399, -13.9142190617628, -10.20989813642594, -19.67318749886311, -13.22545647691756, -11.35738362057711, -10.37800058317319, -9.86308947602663, -20.98168478524144, -5.038213419512004, -12.8612703045419, -23.7103757747438, -25.78805046306136, -29.5117411496098, -15.02489637507387, -32.51478386333478, -15.48689562410333, -23.58179278538965, -10.7011656905293, -12.18338021676437, -11.80719456318334, -34.37559964635795, -21.96698531834351, -15.96606915985646, -18.18645503653203, -23.73685168133605, -15.7426553469114, -11.56446818066272, -21.42813665189797, -23.10666793730778, -24.26053675245742, -14.08444644301535, -23.12886976791419, -13.54997092114479, -24.18202649171034, -13.43311848775762, -18.68125871223531, -14.34963037446899, -21.30807004664649, -11.23675042114956, -20.25521737033718, -11.41928014036639, -23.0616314567799, -12.74836397165115, -8.946938971416877, -21.33592841357732, -18.29022453494306, -23.78096262851221, -10.26615870794974, -23.87195921412485, -7.045007615754844, -27.36975377176551, -13.02213773679562, -24.88461586299227, -9.937370797941819, -20.9215542254461, -13.7430158107626, -13.32781861737069, -16.57378722435969, -13.1562876406111, -18.65461183747465, -12.88434508060274, -25.53251613794421, -23.47076517726, -12.38103504563448, -18.08858152438308, -13.3986078002421, -24.83005553415067, -13.48186232123563, -12.76305322156708, -14.99349220446663, -12.68915386346622, -15.16813193431097, -20.38979714624436, -17.1398617656887, -21.99353054090562, -31.80290581785966, -34.17165493312128, -28.14103833717329, -23.01519425280903, -25.32718282655863, -24.9256764033518, -27.36738567584731, -23.63994953138027, -12.19474154438638, -21.8509764153975, -14.27265880961605, -27.81140090827595, -16.66595175805092, -15.90073698436111, -16.04898816099204, -16.77891193093655, -15.05041271240863, -18.6937096770671, -20.92753847593657, -26.68202074910777, -22.68645320525759, -30.02139727511975, -14.61774067439237, -10.02271219166692, -14.02556111130297, -22.35631047609814, -17.23179491687371, -27.80786897153735, -7.71222261637312, -29.01667081229076, -12.42383366521858, -14.96109424540947, -20.51828142366711, -13.95474218677742, -25.26930987352585, -25.30942633816443, -29.95264501627203, -17.87797633090322, -29.28864522431501, -18.28270560387423, -26.07314333903045, -9.265582530948477, -19.57038320696334, -13.84155482021799, -13.76410195180156, -10.09880900833976, -10.13770828948875, -20.68018631936204]
187 ]
188 },
189 "Evidence Ratios":{
190 "constrained":[
191 [2.987035777683669, 0.9178217737437788, 0.9308445775388399, 5.864129597495543, 3.666988257062931, 40.01921212564599, 1453.329858192022, 46.3517274521344, 6.554313261152158, 0.5242885566486172, 0.1662130613392027, 3.212614540819785, 0.5751533301022933, 1.257440721352396, 1.250089456152151, 0.1833214774704383, 0.3985031341778748, 1.377247408059552, 0.2496560220961017, 0.1986701791114262, 0.2256395217898774, 0.159639393704319, 8.652854738603175, 0.5736394408536711, 1.004422332506298, 2.074674436945399, 4.953543380186865, 2.209813825803168, 6.921262036590584, 0.9507640800590974, 1.100899617321825, 0.5198864839379664, 0.3645685156450084, 17.19714536690562, 0.2328691346279994, 152.2131719709853, 0.5003737786888893, 0.9187491121066572, 0.9487852120654622, 7.883091091521568, 3.337091136584989, 2.784409283932767, 1.669190734679053, 0.8049742711776068, 0.1712690260857312, 22.57426895337745, 1.085372306650974, 0.8865265964983139, 3.407116241547518, 11.54367277296439, 18.59307162257273, 245.2734532644677, 2.187205373636184, 91.65016109978839, 1211.759142055416, 32.71303656181449, 338.4583183795538, 3.958894181734716, 4.679896572127406, 0.8137916933052433, 25.61841393034561, 6.537289569530828, 2.208760315392158, 10.19454391110528, 0.2251760020370068, 0.1724239350018968, 3.568167963566551, 0.2482563079467741, 0.4303489068500915, 0.2358279091453541, 0.2354059080062318, 10.79664683030406, 0.9999999999999982, 0.5312444740983824, 17.02181119579284, 22.93868328909911, 30.04386370541763, 0.3868627537181412, 1740.897204618787, 0.4526354258455894, 8.038038325908458, 0.2604389084082438, 0.5152141115456746, 0.209721521558208, 180.4758697127573, 1.305514179179812, 0.2613067262507715, 1.277036479085304, 4.095891978587106, 2.472733466018775, 0.1714679865462201, 13.4785951464023, 9.293783187007939, 14.73617227655005, 0.2819773273497369, 11.44154239787743, 0.7112330044400204, 9.891163748924974, 0.341307999103254, 2.610863024250461, 0.715183235651846, 12.96323111519599, 0.4429173141007886, 2.410235803025134, 0.3477627964575015, 8.794783055600073, 0.4206486430093566, 0.2644066118480111, 7.29723462938499, 0.1607154811869344, 16.79672116274557, 0.2188413274550005, 56.95216760630651, 0.2328691346279994, 13.2527158196516, 0.1758047062874589, 11.25476432648051, 0.3301128054448652, 3.889129453787352, 0.1929756888698665, 0.6328125582337467, 1.707921865741156, 0.1775006051199708, 1.015876494623396, 0.2146854634782269, 29.58444254980177, 29.41085732710528, 0.1720357129869316, 0.4972444336487338, 0.3116691239926225, 13.00729307176291, 0.5122036510611201, 0.3014085415888103, 1.00026976085985, 0.2354681559800242, 0.5761806291357867, 3.876107182723861, 1.995131941849157, 14.37822484490952, 60.57571835920439, 922.4726067466381, 11.00644544990011, 7.121446858825492, 55.58222702294439, 20.86275396084217, 4.714749185132652, 24.37737183652841, 0.50217828651945, 6.690972854579194, 0.4019946158005773, 46.44301992158756, 4.391292801814232, 0.8276848279024352, 2.907044843855059, 2.908411735743323, 0.5831309060013494, 3.139154092062445, 6.967202141660374, 18.77146096245092, 4.083200457885609, 69.36966574602748, 0.3603034372761033, 0.3494235125609156, 0.1740539474113665, 9.102046375934606, 0.1725097532596096, 116.2237173206706, 0.1967932863167221, 39.57445790025699, 0.3691062038535791, 0.7964541286880364, 16.14101020285773, 0.8193959897025127, 15.41811630139388, 25.20943173776431, 49.06227082795505, 1.576988395869989, 29.11550049727357, 2.947614097314125, 10.29879932442459, 0.1735447747495909, 0.8374832172472122, 0.5829752104000613, 0.8971792315392203, 0.1655725521668218, 0.2367039343819634, 2.407298044116152]
192 ],
193 "optimized null":[
194 [1.249959400407102, 0.9958881520275259, 0.998207509265751, 1.022475766760606, 0.7329779279148643, 0.7355512219978014, 3.215747411518881, 3.831944066897763, 2.992504567232528, 0.8236645230667027, 0.8159500030737468, 1.396476901447714, 0.9750384449114691, 1.16417536866286, 0.2928545373193804, 0.8738264187311083, 1.116680407100678, 1.610657107893188, 1.633098870338358, 1.076295106848796, 1.478341111181925, 1.708669953055735, 0.6501772588199817, 0.8228834033449909, 1.578122886012883, 1.176644073870286, 1.028238233000157, 1.311743164559289, 0.8005936991596435, 0.4612384787800625, 0.4054241751261601, 0.7141843613652971, 1.380541560105011, 0.6731713608501634, 0.932626077339456, 1.376173789613603, 0.6010146384105997, 1.000648214046449, 1.010762802431324, 1.279765846941387, 0.8252095291075795, 0.5488172901332377, 2.905327825256244, 0.4694117092940189, 0.952073347603641, 0.9820568432858974, 0.9684541283622321, 0.7465802831481059, 0.725817575723242, 0.6897980335692911, 0.4519945356959116, 1.644970489890064, 0.6861498379435136, 11.73909248217663, 4.87996237464428, 0.8976824471171899, 2.965984233784409, 0.733133747843722, 0.7183950548657764, 0.6781158778869135, 1.202933169206003, 1.041670940984456, 0.6239400537888191, 0.864005597730941, 0.8863622283336499, 2.211207115702391, 2.415912028974954, 1.558641206543682, 1.178733082401182, 1.144859074170125, 1.052449670353621, 0.9907345967710618, 0.9999999999999973, 1.635182470378155, 0.9532802729006801, 4.075002787751862, 0.7547233152543775, 0.9913306590671749, 10.61305441401069, 1.087472394658304, 2.031666990662131, 0.8935759463782673, 0.7504804700650514, 1.07138642619565, 0.7779921221867564, 0.3692230071631759, 0.5095967222916621, 0.852637781481885, 0.492890538993211, 1.010746910759831, 2.039528413292879, 1.943271153632765, 1.264662551213628, 1.075020419076957, 1.352742324566819, 1.108889296748787, 0.9128213876445376, 1.605270076656883, 0.9963188974862515, 1.369641261789208, 1.110930409345364, 1.759465308015671, 1.041233006895448, 0.7072388659882123, 1.020994825899436, 0.7775662346759626, 1.396238093640341, 1.417000739126258, 1.223497018037751, 0.6592994704264704, 0.7683951448151665, 1.315289046185217, 2.744051160985256, 0.932626077339456, 0.8295939599329692, 1.161718436561281, 1.485979405967741, 1.157190740711233, 0.5180077437805523, 1.005418861153479, 1.872838124227439, 1.909650007781456, 0.9095327119137432, 0.4044301708455042, 1.105326473224138, 1.202728682967098, 1.287402785135559, 1.665642405761295, 0.7767263119192113, 1.006545375541812, 4.958869792471186, 0.8264897380438972, 1.126750821714303, 0.7872722189265667, 1.249979829536444, 0.5392540993266187, 0.900764623315236, 1.480325818230283, 1.853802344884983, 0.8908173136045756, 3.516872648338504, 1.028849304595149, 0.7637780328545294, 1.275961818909257, 1.7479680529214, 0.6149407328711725, 2.288611307253957, 1.143103773111974, 1.134112880938005, 0.6144610028110447, 3.50665225694476, 1.967609019313462, 0.4619393418252924, 1.170835076724906, 0.713460509830789, 0.907767204501339, 0.5897350692995594, 2.180804513956808, 0.6191414671741319, 0.8918751295230388, 1.472219881303941, 0.7738252314079443, 0.9349092081542767, 0.9591890032827355, 2.234571675884028, 0.5165519486568414, 2.268523145559755, 1.592316727559848, 0.9190552183615908, 1.63878552010542, 1.726996028513171, 1.33659173528842, 1.007491351842102, 2.384818706326968, 2.080787852232155, 2.049282389773126, 0.6134033430403113, 1.067413275400906, 1.720346037637947, 0.6260135038640929, 1.365837060781729, 0.4917881296168616, 0.7773205034026993, 0.7635232604405103, 1.969025623887814, 1.950874776061578, 1.759983366341118]
195 ]
196 },
197 "tested":{
198 "0":{
199 "Pig":"test",
200 "Cow":"test",
201 "Node3":"test",
202 "Horse":"test",
203 "Cat":"test",
204 "Node2":"test",
205 "RhMonkey":"test",
206 "Baboon":"test",
207 "Node9":"test",
208 "Human":"test",
209 "Chimp":"test",
210 "Node12":"test",
211 "Node8":"test",
212 "Node1":"test",
213 "Rat":"test",
214 "Mouse":"test"
215 }
216 },
217 "data partitions":{
218 "0":{
219 "name":"busted.filter.default",
220 "coverage":[
221 [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]
222 ]
223 }
224 },
225 "branch attributes":{
226 "0":{
227 "Human":{
228 "original name":"Human",
229 "Nucleotide GTR":0,
230 "MG94xREV with separate rates for branch sets":0,
231 "unconstrained":0,
232 "constrained":0
233 },
234 "Chimp":{
235 "original name":"Chimp",
236 "Nucleotide GTR":0.001818647577470898,
237 "MG94xREV with separate rates for branch sets":0.001828142895085465,
238 "unconstrained":0.001835079043904073,
239 "constrained":0.001827227299324197
240 },
241 "Baboon":{
242 "original name":"Baboon",
243 "Nucleotide GTR":0.001683434956773037,
244 "MG94xREV with separate rates for branch sets":0.001771624553208579,
245 "unconstrained":0.001852571561323465,
246 "constrained":0.001757260248005238
247 },
248 "RhMonkey":{
249 "original name":"RhMonkey",
250 "Nucleotide GTR":0.003773669075849421,
251 "MG94xREV with separate rates for branch sets":0.003717699096857038,
252 "unconstrained":0.003672835047422234,
253 "constrained":0.00373144096412681
254 },
255 "Cow":{
256 "original name":"Cow",
257 "Nucleotide GTR":0.2483322373763571,
258 "MG94xREV with separate rates for branch sets":0.2480141631033857,
259 "unconstrained":0.2960120156157274,
260 "constrained":0.2592686681333873
261 },
262 "Pig":{
263 "original name":"Pig",
264 "Nucleotide GTR":0.187244836750842,
265 "MG94xREV with separate rates for branch sets":0.1926081878751187,
266 "unconstrained":0.2187526946336905,
267 "constrained":0.1943776301130502
268 },
269 "Horse":{
270 "original name":"Horse",
271 "Nucleotide GTR":0.2091766851769093,
272 "MG94xREV with separate rates for branch sets":0.2111575880588217,
273 "unconstrained":0.2572135566477119,
274 "constrained":0.218486450878766
275 },
276 "Cat":{
277 "original name":"Cat",
278 "Nucleotide GTR":0.266381043956941,
279 "MG94xREV with separate rates for branch sets":0.273601177885004,
280 "unconstrained":0.3292215104251173,
281 "constrained":0.28483085314287
282 },
283 "Mouse":{
284 "original name":"Mouse",
285 "Nucleotide GTR":0.1181831744338598,
286 "MG94xREV with separate rates for branch sets":0.1201847378516324,
287 "unconstrained":0.1489713993010398,
288 "constrained":0.1233480139851019
289 },
290 "Rat":{
291 "original name":"Rat",
292 "Nucleotide GTR":0.06669700444436912,
293 "MG94xREV with separate rates for branch sets":0.0670850471739789,
294 "unconstrained":0.07366345007817726,
295 "constrained":0.06713082546371778
296 },
297 "Node1":{
298 "Nucleotide GTR":0.276880831396131,
299 "MG94xREV with separate rates for branch sets":0.2843521449765504,
300 "unconstrained":0.459085769955035,
301 "constrained":0.3115534692518958
302 },
303 "Node12":{
304 "Nucleotide GTR":0.01783434870161725,
305 "MG94xREV with separate rates for branch sets":0.01788794906051452,
306 "unconstrained":0.01828498503175797,
307 "constrained":0.01770410398930177
308 },
309 "Node2":{
310 "Nucleotide GTR":0.06617535490721377,
311 "MG94xREV with separate rates for branch sets":0.06447679597474805,
312 "unconstrained":0.0623969317369398,
313 "constrained":0.06097949807503514
314 },
315 "Node3":{
316 "Nucleotide GTR":0.09884524766349881,
317 "MG94xREV with separate rates for branch sets":0.1017497956116402,
318 "unconstrained":0.1285021744856729,
319 "constrained":0.1065011238088613
320 },
321 "Node8":{
322 "Nucleotide GTR":0.1061610073141143,
323 "MG94xREV with separate rates for branch sets":0.1093806684969149,
324 "unconstrained":0.1348034716617685,
325 "constrained":0.1118205234697939
326 },
327 "Node9":{
328 "Nucleotide GTR":0.02568007351415409,
329 "MG94xREV with separate rates for branch sets":0.02593963430985144,
330 "unconstrained":0.02761127562964508,
331 "constrained":0.02639493109700932
332 }
333 },
334 "attributes":{
335 "original name":{
336 "attribute type":"node label",
337 "display order":0
338 },
339 "Nucleotide GTR":{
340 "attribute type":"branch length",
341 "display order":0
342 },
343 "MG94xREV with separate rates for branch sets":{
344 "attribute type":"branch length",
345 "display order":1
346 },
347 "unconstrained":{
348 "attribute type":"branch length",
349 "display order":0
350 },
351 "constrained":{
352 "attribute type":"branch length",
353 "display order":1
354 }
355 }
356 },
357 "test results":{
358 "LRT":44.77492170961614,
359 "p-value":1.893429857346973e-10
360 }
361 }