diff test-data/busted-out1.json @ 1:a03d87763f51 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
author iuc
date Thu, 13 Feb 2020 15:00:59 -0500
parents 1942d02039c2
children 1fb98a84e86d
line wrap: on
line diff
--- a/test-data/busted-out1.json	Wed Aug 21 12:23:44 2019 -0400
+++ b/test-data/busted-out1.json	Thu Feb 13 15:00:59 2020 -0500
@@ -1,361 +1,394 @@
 {
- "analysis":{
-   "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.",
-   "version":"1.2",
-   "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
-   "authors":"Sergei L Kosakovsky Pond",
-   "contact":"spond@temple.edu",
-   "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})"
+ "Evidence Ratios":{
+   "constrained":    [
+[1.766356514902524, 0.9484374805763239, 0.9571091930814299, 1.845676838710576, 1.513819401189324, 2.11256226458989, 7.366103227625151, 3.937756516229049, 2.586067836907899, 0.722379841928909, 0.3151239046214458, 1.502917468627881, 0.6499879033472316, 1.047489715978757, 1.060206108705189, 0.5038296392390414, 0.8532658611088545, 1.114374823999701, 0.5611409841208096, 0.6702870396165613, 0.4604115167079821, 0.3988433224622866, 2.47019807349414, 0.9858342091732886, 1.106653406611749, 1.067348070135177, 1.77412165088655, 1.321424873505688, 1.90457149631063, 0.7888758683589224, 0.7229203540914775, 0.8813401886687667, 0.6954297746421804, 4.613654710605887, 0.4975309466317643, 1.84565076502724, 0.6214894235132998, 0.9480915704528677, 0.9669462933548731, 1.488081789562878, 1.368539685217942, 1.726522735566884, 1.222915324989829, 0.7085094082639855, 0.3168181005885327, 2.290014391709923, 0.6343005734674315, 0.8841633809961478, 1.508078414734822, 2.666352901083321, 1.732923983135172, 3.102011384229053, 1.585109653073893, 3.345181824497555, 7.193115253213268, 3.850321954428519, 3.233128500312913, 1.977820966308441, 2.047653340750355, 0.6643430465826362, 3.624272911205855, 1.67814994913239, 1.752817561416471, 3.277248182160172, 0.3406457937754578, 0.4841828665456315, 1.399775481724447, 0.5510187898414104, 0.6276769404480749, 0.4535822272441153, 0.4226923979745105, 2.950051361271033, 0.9999999999999982, 1.027733519332009, 2.963278030618241, 2.8935730521221, 1.881916301985038, 0.4490192221083247, 3.102588216900087, 0.7028469232610687, 2.792137897266834, 0.3889955246330017, 0.9360790804326219, 0.4572233386404743, 2.908919410553763, 0.8995968442944373, 0.3261344314757346, 1.080257865601265, 1.399763176607792, 1.534646955858424, 0.4277164444783946, 2.361993404905034, 2.175584822495568, 3.122529901767528, 0.4453847841440882, 1.711825080925545, 0.8458710509917922, 2.741896592382772, 0.576439632416141, 1.142294357680513, 0.8086330800808955, 2.943414796294152, 0.833291758377592, 1.615921141634484, 0.7252129604805458, 2.833655116179036, 0.9138779988368123, 0.6174720822006171, 1.834532902825704, 0.2316812685220093, 2.479235579982967, 0.4643862206171616, 6.530720225707355, 0.4975309466317643, 1.158125132567293, 0.2987944638927862, 3.78696693228073, 0.7343025200073082, 1.93339742618843, 0.3642707474760721, 1.028034824972818, 1.511057897004292, 0.2969890376651506, 0.987605711796378, 0.3709886418939366, 4.185741574214752, 3.002372601666337, 0.424383367760914, 0.4658081554322532, 0.4024556436060775, 2.540164510486854, 0.5199349857684811, 0.4626485320487528, 0.9349816613814522, 0.5525607476128181, 0.5855612460554309, 1.85872747574379, 1.064964125964651, 3.177687923317396, 2.593304657270028, 5.234187858164534, 2.966427299030309, 1.920561682721974, 2.245869881969924, 3.811870935099101, 2.099654636695842, 3.369504334172069, 0.6379165155453101, 3.119867019567397, 0.9211859677702382, 2.195241379859611, 1.767535349740496, 1.225677095999665, 1.347676192394215, 1.671173168407676, 1.179430472478473, 1.873629958128968, 1.972321068578892, 1.863249013159319, 1.501711930393218, 2.85458165498371, 0.5332817404709185, 0.7514817421990073, 0.2887801591578705, 1.93925520496415, 0.2163710715496819, 2.457406602553581, 0.4895227461773333, 2.731573653164397, 0.8923840424261161, 0.6288736610053396, 3.562511382204229, 0.8043427141817341, 2.97831687935463, 3.021636055180988, 1.919432168129229, 1.231674183402057, 3.382911261347008, 1.455440822286478, 1.714894279904311, 0.4763853457361669, 0.907985271671091, 0.9191891327337078, 0.8704988461364657, 0.4660185191281315, 0.6176233729242167, 0.9987767701341157] 
+    ],
+   "optimized null":    [
+[1.118923161648219, 0.9980202548897937, 0.9997654691276022, 1.028326548692021, 0.7919741374095479, 0.6742163346738066, 0.9701775068012184, 1.781350909123149, 2.014615609490285, 0.9375026657270238, 0.6503469909372603, 1.467509823797021, 1.009616470968526, 1.168421464905222, 0.59794016479865, 0.8088642155191522, 0.9570182332372693, 1.200458035608254, 0.9382406902547993, 0.971502044629861, 0.9494035585701087, 0.8642047320556682, 0.7618657208728498, 0.9877802717728724, 1.196913567892764, 1.219008654454505, 1.195602379971315, 1.386927451387816, 0.9612092240804505, 0.7608092856171619, 0.7774974434748834, 0.882472157999228, 1.287408843481257, 0.77835738564002, 0.9105718870056999, 0.9901735448217958, 0.7939955331410506, 1.000490010159418, 1.004589199921733, 1.297516080632708, 1.03030381955465, 0.8106679119008423, 1.81201409338234, 0.7198749295257847, 0.6994440009800842, 0.8437894137548632, 1.143486692785445, 0.9393973334278157, 0.8256667500261211, 0.7815159607314222, 0.5985208951864024, 0.8535790889335229, 1.025460140178824, 3.820941298927726, 1.291930691854327, 0.9067539623849099, 1.157350624394714, 0.998318955418969, 0.9161866303121252, 0.8876780413980894, 1.109157480575484, 1.092621268372832, 0.8972624848442422, 0.9889106716665784, 0.8341566095527148, 1.038544978108518, 1.714787775296502, 0.9137222760182561, 1.034926570525361, 0.8813745500117369, 0.8349529524516258, 1.213599287773434, 1, 1.089476250837934, 0.8899148576721072, 2.300141517859181, 0.6825541016975851, 1.003665786880968, 1.237110533718188, 1.020075909706045, 1.638150182736532, 0.9011618842606461, 0.9230020461155208, 0.751689080395277, 0.5897676439072257, 0.6404917862661024, 0.7469389376638015, 1.083533646483151, 0.7344437672842805, 1.131725226416453, 0.9190373093865288, 1.470665196381038, 1.267251236251085, 1.076738563303299, 0.9719321192139432, 1.046564634995135, 1.040861206200881, 1.432126587856311, 0.9607511063877517, 1.317983216727182, 1.009193498305615, 1.490294304430241, 0.9453834990966208, 0.9949520064421568, 0.9321847062820814, 1.012192223349541, 1.006095335695502, 1.015717182050207, 1.155947081675256, 0.7426317882836824, 0.8600656083242881, 0.8659102843696671, 2.043199066063688, 0.9105718870056999, 0.7755680708217269, 0.8691797858502243, 1.408772939677855, 0.9935920773928444, 0.776611704010421, 0.7417817446846022, 1.113087499879386, 1.540328788060018, 0.7887000169650941, 0.7125843942768558, 0.803768142354686, 1.030948607017191, 1.106410103708125, 0.8462900614413438, 0.9257201660506196, 0.9862223424699452, 2.874290057428853, 0.9765125041895547, 0.9522206558439166, 0.979008503258283, 0.8163413206500215, 0.7929865064112649, 1.054431661259741, 1.391867727782659, 1.55344883290767, 0.9159617667614252, 1.37597067666192, 1.180188215894089, 0.8980539087871242, 0.8445482715276972, 1.439858975048729, 0.8167533472760263, 1.611375099688448, 0.9949969190225336, 1.453373381083946, 0.8294327035809631, 1.883890801528407, 1.621067636191696, 0.7786019875784795, 1.241031199394852, 0.8699818919359624, 0.8969821406492622, 0.8552871694200248, 1.476143154036665, 0.7328425886346202, 1.12339872066542, 1.055700479953033, 0.8643592588676906, 0.8828252272762036, 0.8310350398630689, 1.509625875333898, 0.8258835645292275, 1.192338427340326, 0.988317199275236, 0.7869748564877793, 1.092663634718098, 1.540873058588039, 1.27733975846824, 1.071338379207414, 1.598643725487392, 2.039697563641063, 1.125982095744282, 0.8865373778453701, 0.896677110067575, 1.480314453817297, 0.6279749170263321, 0.9454481522954102, 0.8270407761576262, 0.924976567928722, 0.9460839037512674, 1.00781396274934, 1.11935672287797, 1.612656256447746] 
+    ]
   },
- "input":{
-   "file name":"/Users/stephenshank/Documents/Galaxy/tools-iuc/tools/hyphy/test-data/absrel-in1.fa",
-   "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)"
-    }
+ "Site Log Likelihood":{
+   "constrained":    [
+[-10.45729861177352, -3.484017570185021, -3.811593093827024, -18.53808870245015, -17.92309552060635, -29.83947832086448, -32.51456888432799, -26.14022567456645, -18.98957484098232, -10.33347856776535, -16.45292539731993, -23.86010381033633, -20.00687543711394, -16.65179796964098, -21.99232160499268, -12.26652073720412, -10.69225356932102, -15.60314346893525, -11.01132866125176, -8.521297155687831, -8.203139397826641, -11.43545706508415, -24.90046120971902, -13.6386798900763, -14.85763270108216, -14.7030317250254, -22.05138318385674, -15.98662844335023, -21.8003647511144, -18.57068156644835, -22.299055200187, -14.20074227547402, -10.45246619974257, -29.65657150543187, -5.937537382195638, -33.78920222670538, -15.44637827577353, -4.279026884494699, -4.808492102928678, -24.63079311886252, -19.95624962482634, -20.75045752192579, -12.74902310767432, -18.99427847476613, -14.28731466672857, -24.54528292419485, -16.76361995667699, -15.30372003397147, -21.15548703165981, -23.72245288385755, -28.94171761244187, -31.14183824690388, -20.64762811392306, -24.08520562625058, -32.41122173355103, -27.15825647361205, -28.5179867447387, -21.82691317662457, -23.87561847496401, -15.96134254249656, -22.91741429446779, -22.8344267349475, -18.86994129807232, -24.15268806222941, -13.09988257350861, -6.987933615627104, -20.27062516100397, -11.6267899578313, -10.76199226925333, -9.365202828107813, -8.830802980942332, -22.25274148442388, -5.072420031658066, -11.5940578599292, -24.90254274563229, -26.4504338975355, -29.4914117779418, -14.39917492841001, -30.20915692724294, -15.07835940842867, -24.47922859714559, -9.963108156848188, -12.02484522350882, -10.47082266101894, -32.61997541577167, -22.41917549927993, -15.45008408736274, -18.58952738985428, -24.90070817016433, -16.46583864612196, -9.349881275491541, -21.92481437356786, -23.89225210843373, -25.41089239829785, -13.11222485538043, -23.55550258653596, -13.5386142710809, -25.36851139033049, -12.93730850270479, -18.80108927581331, -14.23685164495206, -22.26383266334966, -10.55622492327747, -21.48906087213606, -10.38853588609826, -24.53689740053753, -11.36767104821917, -6.908653364620656, -21.84280151068446, -17.93716231251139, -24.46209768558333, -8.752467536320703, -25.50970610456629, -5.937537382195638, -26.74893035287963, -11.9403240118369, -26.13347920733979, -8.842765208651075, -22.25304376265024, -12.64504365092861, -11.95155411820952, -16.44565617489921, -12.21136817821285, -19.4495506152908, -12.03636955134022, -26.76158975846396, -24.28299039768532, -10.41253856833306, -18.04928878164386, -12.66411737564947, -24.89370230796465, -13.28589560426102, -12.14998856202217, -15.22485748978356, -11.10445442252986, -15.26584291199847, -21.18251113737594, -17.4492424252813, -22.91858352137089, -32.12984803882419, -34.72655653940613, -29.46637589613799, -23.83622026476351, -25.19174747094332, -26.15371116437007, -28.38602800921473, -24.3904479288928, -11.83470465315949, -22.99304711962677, -14.1052741197831, -27.4333232450484, -16.96102482386623, -16.48031664612245, -16.51933846935232, -17.67884199792057, -14.76033658655028, -19.64011886967656, -21.73563121093473, -27.07964360348662, -23.31227029359847, -30.36351219328728, -14.39405059091475, -9.0012985358923, -13.02696101249317, -22.60078004596954, -16.83684027122174, -27.58316083045541, -5.435892920303646, -29.48238449481695, -10.75922123674425, -14.39572297485616, -21.65465418121673, -13.81883365226544, -26.28515446199947, -25.94713203139664, -30.32048162447653, -18.74338069598867, -29.89507747948719, -18.59896471825973, -26.6197512688528, -7.057151084653121, -20.11123180495239, -13.68737039495877, -13.8591446292234, -7.100328940735415, -7.27389954199287, -20.4341543043075] 
+    ],
+   "optimized null":    [
+[-10.000746412889, -3.534975268563031, -3.855196330132343, -17.9531754129423, -17.27523311609171, -28.69737251844359, -30.487403824811, -25.3469865397239, -18.73986474128691, -10.5941470716412, -17.17746554049388, -23.83626257910331, -20.44724749063709, -16.76105507711494, -21.41959368469256, -12.7399136042534, -10.80700483642069, -15.67755309754298, -11.52536299421752, -8.892434491135736, -8.926852661062641, -12.20869809997624, -23.72417791244537, -13.64065197048924, -14.93603840556554, -14.8358925422005, -21.65672787001029, -16.03500867314082, -21.11654452541332, -18.53445530201509, -22.37183650032519, -14.20202582413271, -11.06832299336804, -27.87698168792971, -6.541952472626266, -33.16649523981481, -15.69133721810966, -4.332820962725578, -4.846683129097396, -24.49375694739045, -19.67235910587276, -19.99445132707328, -13.14222447425636, -19.010192624522, -15.07927260784268, -23.54687249677092, -17.35293440007094, -15.36431670327766, -20.55308672706422, -22.49522159373395, -27.87861362498808, -29.85147043539681, -20.21211595634147, -24.21818138264384, -30.69423513967148, -25.71221557332896, -27.49066994877449, -21.14323500088168, -23.07138885914685, -16.25115300126723, -21.73336130310753, -22.40531441170235, -18.20030993527343, -22.95453268750557, -13.99546052997636, -7.751046909853225, -20.47360263421817, -12.13254771763505, -11.26205241801605, -10.02950893550899, -9.511533636871842, -21.36450946580444, -5.072420031658067, -11.65239902588355, -23.69961716091314, -26.2209124593937, -28.47720772549854, -15.20352359389407, -29.28969870111495, -15.45085261296868, -23.94598869120682, -10.80322523133013, -12.0107767142687, -10.96797346503774, -31.02416709659281, -22.07946508441355, -16.27875786287543, -18.59255520779903, -24.25576326194178, -16.16128150518837, -10.11474753171002, -21.45102326094385, -23.35180477003816, -24.34618548249837, -13.89257222918985, -23.06345551040454, -13.74605107743702, -24.71902198635289, -13.44815326344599, -18.94415314361011, -14.45841315258903, -21.58323588087952, -10.68243175660201, -21.00409493400298, -10.63960151353855, -23.50744845859135, -11.46380607942174, -7.40636973341585, -21.38093160255466, -19.10200007557443, -23.40340080290285, -9.37553226377444, -24.34770562165953, -6.541952472626266, -26.34796839682552, -13.00811807862387, -25.1446328603122, -9.145170849858582, -21.34095019187551, -13.35620130330373, -12.03104276076478, -16.46484206770943, -13.18805899222384, -19.12316542756082, -12.80950895147612, -25.36038522816893, -23.28470818774974, -11.10276351543467, -18.73608690839096, -13.56041431572836, -25.01727916833232, -13.9161793832148, -12.87181769553462, -15.27087090233286, -11.49472359736922, -15.56907833534053, -20.61562094868151, -17.71694784548008, -22.20290716981454, -31.08913439244855, -33.39050427276854, -28.54469152779638, -23.07607739799698, -24.21370116505611, -25.18013621147851, -27.44183700650422, -23.65277019084076, -12.27923687244804, -22.22914406475213, -14.0003541619513, -27.28037045002411, -16.87452367228698, -16.02656793234758, -16.4368993455096, -17.02603324065743, -14.48658558781633, -18.85592317056478, -21.445852863631, -26.14649750870843, -23.02202321164394, -29.3687914002132, -14.87698920390545, -9.162378872547357, -14.08396726867812, -22.35033791702401, -18.17629921418486, -26.85997070710383, -6.138465689345856, -28.23794764233195, -10.96169835180006, -15.29189705116706, -20.62896804216628, -14.10547218000938, -25.66295172482926, -25.55413515032033, -29.78710785677539, -18.41457433641119, -28.56728137258359, -18.61591042688218, -25.61514478015318, -7.742583058377544, -20.01785764703301, -13.69364689624316, -13.94240945383619, -7.871642437614435, -7.868530143948813, -20.91326095114609] 
+    ],
+   "unconstrained":    [
+[-9.888379652897939, -3.536956975958899, -3.855430888511407, -17.92524264198113, -17.50845965857853, -29.09157676668757, -30.51768005233528, -24.76961452555787, -18.03943632860708, -10.65868274934065, -17.60771476681289, -23.45269561216572, -20.4376769636146, -16.6054014145564, -21.93385827359542, -12.9520378226385, -10.85093767163684, -15.49484991723633, -11.58911175769067, -8.921346396691311, -8.978773985704009, -12.35464367982677, -23.99616287059628, -13.65294697344841, -14.75629218887099, -14.63785459209203, -21.4780777279763, -15.70791783931325, -21.15610770415758, -18.80782786477065, -22.62351142339454, -14.32705386381445, -10.81569144349841, -28.12755118363321, -6.63563490222878, -33.17637029323138, -15.92201466162742, -4.332331072581934, -4.842104427446767, -24.23330521785812, -19.64250537668504, -20.20434811557675, -12.547785488861, -19.33887041557516, -15.4367421517065, -23.71672482205896, -17.21885230292473, -15.42683344726171, -20.74465076426493, -22.74174129986231, -28.39190746698947, -30.00978751219203, -20.18697452723667, -22.87768457704827, -30.43809737982556, -25.8100997042818, -27.34453650032288, -21.14491746000365, -23.1589240493258, -16.37029916899328, -21.62976060249833, -22.31673476907595, -18.30871676975877, -22.9656839608183, -14.17679464299017, -7.713226235808525, -19.93431330744026, -12.22277632689638, -11.22772194016784, -10.15578153700462, -9.691913536959838, -21.17091890362336, -5.072420031658067, -11.56670194893985, -23.81624664728228, -25.38794180884747, -28.85912121067668, -15.19986450963457, -29.07692025541677, -15.43097556716119, -23.45242102332656, -10.90729559707754, -12.09090054194056, -11.25340596248809, -31.55219374013023, -22.52498406608164, -16.57052970348788, -18.51232761277223, -24.56440510741808, -16.03753828771942, -10.19917609135148, -21.06530844796211, -23.11495459612987, -24.27224885909952, -13.92104154234985, -23.01794248639294, -13.70600262406975, -24.35986152238043, -13.48819316139627, -18.66805044150527, -14.4492616572491, -21.18426226067477, -10.73859637126286, -21.00915571172136, -10.7098258147646, -23.49532996174187, -11.45772924514136, -7.390774787133855, -21.23601161044981, -19.39955500699172, -23.5541474067981, -9.519506237286315, -23.6331888724584, -6.63563490222878, -26.60212792035497, -13.14832336553394, -24.80191379036194, -9.151599391331736, -21.5937649828387, -13.65490152701742, -11.92390507531763, -16.03284617533124, -13.42542822929183, -19.46202235330671, -13.02795338302471, -25.32990587208053, -23.18358755436579, -11.26965663135059, -18.81327019488709, -13.57428776606662, -23.96147346112334, -13.93994710685256, -12.92077618523389, -15.29208585316513, -11.69764632373376, -15.80102740870741, -20.56261903661609, -17.38630131122748, -21.76242965716022, -31.17691504697109, -33.07134484404992, -28.37901759704339, -23.18360257842184, -24.38265454953325, -24.81559103668038, -27.64425513672643, -23.17568227719417, -12.28425251073614, -21.85525674064724, -14.18736746348983, -26.64703123652192, -16.39143870542445, -16.27682322339721, -16.22095669907547, -17.16531612207426, -14.59530491502789, -19.01224116633539, -21.05642015432602, -26.45732185834116, -22.90566454933433, -29.31458689156966, -15.02275599163344, -9.287006901120908, -14.26905058779356, -21.93847606157545, -18.36760069262192, -26.6840542632031, -6.150217270208246, -28.47750662196133, -10.87307993496604, -14.85954787421955, -20.38418844062237, -14.03656349147213, -25.19379612663061, -24.84133360657191, -29.66845222794427, -18.53500632737776, -28.67634082079026, -18.22365589287899, -26.08039983450566, -7.798679287046689, -20.20775892609134, -13.77163377000268, -13.9978334745163, -7.863858845763236, -7.755775978219822, -20.4353782829297] 
+    ]
+  },
+ "Synonymous site-posteriors":  [
+[0.08576487129701713, 0.2936722378990316, 0.2901632602723997, 0.01635516164580625, 0.0171445713661009, 0.000329807826277061, 2.384037236058195e-06, 0.003474937198538037, 0.1657001102485818, 0.4931122461392571, 0.6116781976326224, 0.1232572132258079, 0.3167287850643093, 0.3360418775747802, 0.09625774163526932, 0.7077210076579118, 0.8230716605433912, 0.4692840075680767, 0.8542599193835906, 0.8678806224860721, 0.7187694305926973, 0.8652759434333591, 0.006733209198735493, 0.5563418685268529, 0.548770039188077, 0.1117221464925625, 0.06375767530950946, 0.2544248885020188, 0.01241307080226442, 0.06415938924723534, 0.0664819611257975, 0.5678603832955883, 0.5701480360753304, 0.01716185680432071, 0.7450690448837864, 4.340363369344909e-06, 0.1054553312659123, 0.2962973099054295, 0.2887729969101556, 0.002139003370945352, 0.009013172357941268, 0.1358034694997206, 0.4571022356539327, 0.03050258030555141, 0.6104018187033817, 0.0009310184681936825, 0.05125568890333056, 0.2012729288816644, 0.02168623857883216, 0.005190644975220393, 0.0003844182663365903, 2.025101452550204e-05, 0.2653166678500586, 0.002736950624682267, 4.330160538654619e-05, 0.002447017669235062, 1.04185776899838e-05, 0.07686655084745994, 0.04255051609568109, 0.07964927182431392, 0.009868735494425898, 0.003987427214854124, 0.1864468621560382, 0.02614830208528422, 0.339871175815004, 0.9584270556742166, 0.1208451401789099, 0.8379535111570964, 0.4399112612280809, 0.6546600093353926, 0.6014957564153406, 0.03692874096493579, 0.2645541257391173, 0.877048492043487, 0.005212760236057918, 0.02626182426280086, 0.0003466347596566336, 0.2143323363123782, 3.94830951316172e-06, 0.4695770030113981, 0.141253166719253, 0.287277996900563, 0.529618089155993, 0.7751260138271018, 1.589794382004903e-06, 0.01061110460382564, 0.06904202423665572, 0.1222752760738798, 0.009436108368219053, 0.1756755023547773, 0.8674741705013883, 0.006953150480735887, 0.01485544007614186, 0.01061671400804696, 0.4622922362107368, 0.006976448397641074, 0.2288428608566239, 0.04492921236889752, 0.4792814192644717, 0.08021780746327278, 0.4272287756026639, 0.04187262145239815, 0.7448375318386113, 0.1041516052437809, 0.7758641911259492, 0.04153272254198651, 0.8730527081784645, 0.9061533002525032, 0.007394637725624075, 0.3286876779500328, 0.003007591552118394, 0.7696698519008212, 0.01472154002347215, 0.7450690448837864, 0.0002833970218347724, 0.4752847620805873, 0.06772419306275075, 0.7916442061973822, 0.04768815546756307, 0.633646799271313, 0.8506170933861232, 0.5333086229236574, 0.4601664067609844, 0.1298585434125494, 0.5258807564626594, 0.004910934759931754, 0.005326392789739794, 0.8568922356649976, 0.1781177185740091, 0.2618990376844352, 0.02043267281856545, 0.1513767944689721, 0.390161257271147, 0.2016761548930196, 0.862737391517766, 0.08518368394903716, 0.08643358463113204, 0.05626956022636653, 0.01204362533281676, 0.0001127787870965998, 9.187529415014566e-05, 0.0291337834475492, 0.00445510836740222, 0.000433375749053344, 0.01045459853680832, 0.02886192573391665, 0.01378875281992316, 0.419096617458437, 0.08903224698878176, 0.6525609111129962, 0.000772784141393912, 0.1484449334606463, 0.3645995750997711, 0.1075676751865187, 0.05248459777601974, 0.760566182374103, 0.09207060671403174, 0.05268528446916099, 0.0009595976424648991, 0.01801675181476272, 0.0003997370600438763, 0.4402401340454297, 0.7531135804916973, 0.4676233954749258, 0.006368990121970666, 0.1181278057317597, 0.0001342462574260838, 0.9089018067832817, 0.0004345263536072176, 0.8867574663987829, 0.3111239693194546, 0.02252285354211625, 0.2512560362419685, 0.02269736493711449, 0.006974745835283193, 0.001246559659240012, 0.1018711078071347, 0.001887551089155725, 0.1122951541441214, 0.003158025675593529, 0.9204927908967985, 0.262934005368038, 0.5690451557167514, 0.2158987219764257, 0.9551133675001365, 0.9600236276711078, 0.02872243122605889],
+  [0.6588352549067005, 0.6300104042707274, 0.6308571396167474, 0.7628498871463081, 0.8812042447619804, 0.6450891271407698, 0.05702739009473294, 0.9052573432113765, 0.8322529842816521, 0.50204312688312, 0.3866851002627893, 0.8747673220745895, 0.6811185218928401, 0.6610720252813483, 0.8929509703524842, 0.2915251071042961, 0.176811569233057, 0.5263591043980159, 0.1456890777980846, 0.1319463960095295, 0.2805572096643838, 0.1345797208549885, 0.9194135193694579, 0.4431254580098209, 0.4501541421700466, 0.8327692240155901, 0.9249414026465288, 0.7390951865327187, 0.8744353425012321, 0.9003053400605937, 0.8607595493014167, 0.4302521815275474, 0.4286513165586879, 0.9642067966077235, 0.2534046915188728, 0.08697751816092071, 0.8792501564264749, 0.629642009566426, 0.6314100395448802, 0.7743277052937813, 0.9104949339617914, 0.840440805697928, 0.5404779055776763, 0.9347773671807053, 0.38755746509272, 0.803369306230527, 0.8966425612886076, 0.7886475139801737, 0.8907941079713984, 0.9190014978832025, 0.3522378332471661, 0.1809014504433939, 0.7336944853537225, 0.679888350179917, 0.1899336275352233, 0.791565555728643, 0.1067866556887754, 0.8860612799729447, 0.9367096223134744, 0.8639495448862111, 0.8782437507986685, 0.8302753492657331, 0.809246382642996, 0.9489076442875167, 0.6454229523694828, 0.04155980960796609, 0.8665041382416315, 0.1619827626792043, 0.5565828858468974, 0.3438258751795431, 0.3942275346898335, 0.9283744290898972, 0.6325830460054775, 0.122929910215236, 0.7522797532502616, 0.8972993534299837, 0.4731648184244552, 0.7708474985702127, 0.1508465096375764, 0.5295553683583388, 0.8547957966471971, 0.7024691755465428, 0.4684299719444062, 0.2244610051764785, 0.06738333747301979, 0.9145680765086048, 0.8503190574296829, 0.8699211983668487, 0.9075726506652723, 0.8125612641935661, 0.1324109903321076, 0.8515026484303992, 0.8666935506701156, 0.9245019813561807, 0.5361574183136518, 0.8308943234035726, 0.7647222555512423, 0.9159763441092864, 0.5190913963288092, 0.8928229399251451, 0.5707529496400237, 0.9343160770300315, 0.2547839947945623, 0.8913151216228844, 0.223496387182918, 0.9013900066737581, 0.126912980063931, 0.0938116230998244, 0.8835051043478275, 0.6624762956118966, 0.6292629647931889, 0.2299240837554979, 0.9695268312861339, 0.2534046915188728, 0.5777582640025832, 0.5191726594909567, 0.9265362606441389, 0.2079933538642454, 0.9349466692539032, 0.3655144546780216, 0.1493401333693624, 0.4664213351146896, 0.5331210003016799, 0.8598519162876399, 0.4720884356129527, 0.8952518575745732, 0.7912019413079115, 0.1429432971101487, 0.7981491417404037, 0.7282408814095576, 0.9567712858079624, 0.8212946734056131, 0.6074315581830233, 0.7856999935768023, 0.1372238635707822, 0.8761504406261441, 0.9040762460981876, 0.9081517064494045, 0.9474670754436387, 0.281231292023929, 0.3390927372020315, 0.9480257660647574, 0.8311989201224447, 0.5366551813586112, 0.9375431236313668, 0.9623354548612517, 0.9580572325538602, 0.5752668110481099, 0.9087426219429084, 0.3468515258883331, 0.7120456179760087, 0.8415949727501237, 0.633421707019731, 0.8728889518506465, 0.8967713999817422, 0.2393218619503596, 0.8909502607437078, 0.9247399939031163, 0.7113741304335964, 0.9516574813231364, 0.6065518446899986, 0.5559651751026748, 0.2462092450152424, 0.5251860236577571, 0.8626393300473802, 0.8553625770855506, 0.4554509237222495, 0.09096122393915286, 0.529780817243299, 0.1132163886582516, 0.6816431744145428, 0.9362134283263105, 0.7412706566370515, 0.9244285156386869, 0.8902138302828968, 0.5906194062496973, 0.8830436003628626, 0.8234964935583747, 0.8823463108045396, 0.8452618508291229, 0.07941357187491897, 0.7357914877268877, 0.4290296557540788, 0.7740804045679049, 0.04487007138865241, 0.03997374347326944, 0.912296929053887],
+  [0.2553998737962824, 0.07631735783024095, 0.07897960011085291, 0.2207949512078856, 0.1016511838719186, 0.3545810650329531, 0.942970225868031, 0.09126771959008544, 0.002046905469766074, 0.004844626977622985, 0.001636702104588283, 0.001975464699602527, 0.002152693042850789, 0.002886097143871596, 0.01079128801224668, 0.0007538852377919047, 0.0001167702235517668, 0.00435688803390722, 5.1002818324778e-05, 0.0001729815043981829, 0.0006733597429191042, 0.0001443357116525265, 0.07385327143180669, 0.0005326734633262727, 0.001075818641876393, 0.05550862949184748, 0.01130092204396166, 0.006479924965262574, 0.1131515866965035, 0.03553527069217096, 0.07275848957278573, 0.001887435176864453, 0.001200647365981756, 0.01863134658795579, 0.001526263597340909, 0.9130181414757098, 0.01529451230761291, 0.07406068052814456, 0.07981696354496427, 0.2235332913352734, 0.08049189368026742, 0.02375572480235134, 0.002419858768391037, 0.03472005251374328, 0.002040716203898256, 0.1956996753012791, 0.05210174980806165, 0.01007955713816182, 0.08751965344976946, 0.07580785714157701, 0.6473777484864973, 0.8190782985420806, 0.0009888467962190556, 0.3173746991954007, 0.8100230708593901, 0.2059874266021218, 0.8932029257335347, 0.03707216917959535, 0.02073986159084442, 0.05640118328947497, 0.1118875137069056, 0.1657372235194127, 0.004306755200965905, 0.02494405362719899, 0.01470587181551327, 1.31347178174259e-05, 0.01265072157945855, 6.372616369940412e-05, 0.003505852925021835, 0.001514115485064287, 0.004276708894825967, 0.03469682994516703, 0.102862828255405, 2.159774127705953e-05, 0.2425074865136805, 0.07643882230721545, 0.5264885468158881, 0.01482016511740909, 0.8491495420529105, 0.0008676286302631026, 0.00395103663354991, 0.01025282755289429, 0.001951938899600739, 0.0004129809964198562, 0.9326150727325982, 0.07482081888756961, 0.08063891833366137, 0.007803525559271599, 0.08299124096650871, 0.01176323345165673, 0.0001148391665040469, 0.1415442010888649, 0.1184510092537426, 0.06488130463577248, 0.001550345475611415, 0.1621292281987863, 0.006434883592133867, 0.0390944435218161, 0.001627184406719129, 0.02695925261158226, 0.002018274757312532, 0.02381130151757035, 0.0003784733668262425, 0.004533273133334742, 0.0006394216911327579, 0.05707727078425542, 3.43117576046495e-05, 3.507664767224504e-05, 0.1091002579265486, 0.008836026438070649, 0.3677294436546928, 0.0004060643436808472, 0.01575162869039373, 0.001526263597340909, 0.4219583389755819, 0.005542578428455856, 0.005739546293110378, 0.0003624399383724484, 0.01736517527853375, 0.0008387460506655657, 4.277324451437318e-05, 0.0002700419616530316, 0.006712592937335689, 0.01028954029981052, 0.002030807924387894, 0.09983720766549499, 0.2034716659023486, 0.0001644672248535993, 0.02373313968558726, 0.009860080906007207, 0.0227960413734721, 0.02732853212541473, 0.002407184545829678, 0.01262385153017814, 3.874491145169847e-05, 0.0386658754248187, 0.009490169270680476, 0.03557873332422891, 0.04048929922354462, 0.7186559291889745, 0.6608153875038184, 0.02284045048769326, 0.1643459715101531, 0.4629114428923355, 0.0520022778318248, 0.00880261940483151, 0.02815401462621663, 0.005636571493453016, 0.002225131068309814, 0.0005875629986705686, 0.2871815978825973, 0.009960093789229935, 0.001978717880497971, 0.01954337296283469, 0.05074400224223814, 0.0001119556755373595, 0.01697913254226044, 0.02257472162772266, 0.2876662719239387, 0.03032576686210087, 0.3930484182499576, 0.003794690851895586, 0.0006771744930604194, 0.007190580867317107, 0.1309916798306492, 0.02650961718268966, 0.5444148300203245, 0.0001369692775655127, 0.4697846564030937, 2.614494296533173e-05, 0.007232856266002665, 0.0412637181315732, 0.007473307120980099, 0.05287411942419848, 0.10281142388182, 0.4081340340910627, 0.01508529183000272, 0.1746159553524696, 0.005358535051338847, 0.1515801234952836, 9.36372282825981e-05, 0.00127450690507435, 0.001925188529169687, 0.01002087345566931, 1.656111121114513e-05, 2.628855622720807e-06, 0.05898063972005398] 
+  ],
+ "analysis":{
+   "authors":"Sergei L Kosakovsky Pond",
+   "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
+   "contact":"spond@temple.edu",
+   "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted \njointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. \nAssuming there is evidence of positive selection (i.e. there is an omega > 1),  BUSTED will also perform a quick evidence-ratio \nstyle analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, \nand relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2). Version 2.1 adds a grid search for the initial starting point.\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. Version 3.0 implements the option\nfor branch-site variation in synonymous substitution rates\n",
+   "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
+   "version":"3.0"
   },
  "background":0,
- "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
-    },
-   "MG94xREV with separate rates for branch sets":{
-     "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
-    },
-   "Unconstrained model":{
-     "Log Likelihood":-3437.188861487313,
-     "estimated parameters":35,
-     "AIC-c":6945.751768776152,
-     "Rate Distributions":{
-       "Test":{
-         "0":{
-           "omega":0.1052869846173941,
-           "proportion":0.2379046712842726
-          },
-         "1":{
-           "omega":0.2107329369900513,
-           "proportion":0.4121351840538361
-          },
-         "2":{
-           "omega":3.951290720456698,
-           "proportion":0.3499601446618912
-          }
-        }
-      },
-     "display order":2
-    },
-   "Constrained model":{
-     "Log Likelihood":-3459.576322342121,
-     "estimated parameters":34,
-     "AIC-c":6988.449647409037,
-     "Rate Distributions":{
-       "Test":{
-         "0":{
-           "omega":0,
-           "proportion":0.1368169359858254
-          },
-         "1":{
-           "omega":0,
-           "proportion":0.09947859848803366
-          },
-         "2":{
-           "omega":1,
-           "proportion":0.7637044655261409
-          }
-        }
-      },
-     "display order":3
-    }
-  },
- "timers":{
-   "Overall":{
-     "timer":79,
-     "order":0
-    },
-   "Preliminary model fitting":{
-     "timer":22,
-     "order":1
-    },
-   "Unconstrained BUSTED model fitting":{
-     "timer":29,
-     "order":2
-    },
-   "Constrained BUSTED model fitting":{
-     "timer":18,
-     "order":3
-    }
-  },
- "Site Log Likelihood":{
-   "unconstrained":[
-    [-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]
-    ],
-   "constrained":[
-    [-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]
-    ],
-   "optimized null":[
-    [-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]
-    ]
-  },
- "Evidence Ratios":{
-   "constrained":[
-    [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]
-    ],
-   "optimized null":[
-    [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]
-    ]
-  },
- "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":"busted.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,
-       "MG94xREV with separate rates for branch sets":0,
-       "unconstrained":0,
-       "constrained":0
-      },
-     "Chimp":{
-       "original name":"Chimp",
-       "Nucleotide GTR":0.001818647577470898,
-       "MG94xREV with separate rates for branch sets":0.001828142895085465,
-       "unconstrained":0.001835079043904073,
-       "constrained":0.001827227299324197
-      },
      "Baboon":{
+       "MG94xREV with separate rates for branch sets":0.001771850913718116,
+       "Nucleotide GTR":0.00167976779100812,
+       "constrained":0.0005055252388761481,
        "original name":"Baboon",
-       "Nucleotide GTR":0.001683434956773037,
-       "MG94xREV with separate rates for branch sets":0.001771624553208579,
-       "unconstrained":0.001852571561323465,
-       "constrained":0.001757260248005238
-      },
-     "RhMonkey":{
-       "original name":"RhMonkey",
-       "Nucleotide GTR":0.003773669075849421,
-       "MG94xREV with separate rates for branch sets":0.003717699096857038,
-       "unconstrained":0.003672835047422234,
-       "constrained":0.00373144096412681
-      },
-     "Cow":{
-       "original name":"Cow",
-       "Nucleotide GTR":0.2483322373763571,
-       "MG94xREV with separate rates for branch sets":0.2480141631033857,
-       "unconstrained":0.2960120156157274,
-       "constrained":0.2592686681333873
-      },
-     "Pig":{
-       "original name":"Pig",
-       "Nucleotide GTR":0.187244836750842,
-       "MG94xREV with separate rates for branch sets":0.1926081878751187,
-       "unconstrained":0.2187526946336905,
-       "constrained":0.1943776301130502
-      },
-     "Horse":{
-       "original name":"Horse",
-       "Nucleotide GTR":0.2091766851769093,
-       "MG94xREV with separate rates for branch sets":0.2111575880588217,
-       "unconstrained":0.2572135566477119,
-       "constrained":0.218486450878766
+       "unconstrained":0.0005398732671668005
       },
      "Cat":{
+       "MG94xREV with separate rates for branch sets":0.2738959056554072,
+       "Nucleotide GTR":0.266075486389923,
+       "constrained":0.1152712488116292,
        "original name":"Cat",
-       "Nucleotide GTR":0.266381043956941,
-       "MG94xREV with separate rates for branch sets":0.273601177885004,
-       "unconstrained":0.3292215104251173,
-       "constrained":0.28483085314287
+       "unconstrained":0.120218071527276
+      },
+     "Chimp":{
+       "MG94xREV with separate rates for branch sets":0.001827968855137289,
+       "Nucleotide GTR":0.001817801565830578,
+       "constrained":0.0006181497274348637,
+       "original name":"Chimp",
+       "unconstrained":0.0006183542388399873
+      },
+     "Cow":{
+       "MG94xREV with separate rates for branch sets":0.2477119781238836,
+       "Nucleotide GTR":0.2480176045457076,
+       "constrained":0.1036665344622347,
+       "original name":"Cow",
+       "unconstrained":0.1088268022245659
+      },
+     "Horse":{
+       "MG94xREV with separate rates for branch sets":0.211203801568566,
+       "Nucleotide GTR":0.2090856782081004,
+       "constrained":0.08236651201101133,
+       "original name":"Horse",
+       "unconstrained":0.08564084427400141
+      },
+     "Human":{
+       "MG94xREV with separate rates for branch sets":0,
+       "Nucleotide GTR":0,
+       "constrained":0,
+       "original name":"Human",
+       "unconstrained":0
       },
      "Mouse":{
+       "MG94xREV with separate rates for branch sets":0.1200702443392807,
+       "Nucleotide GTR":0.1181301915748399,
+       "constrained":0.04601717170435755,
        "original name":"Mouse",
-       "Nucleotide GTR":0.1181831744338598,
-       "MG94xREV with separate rates for branch sets":0.1201847378516324,
-       "unconstrained":0.1489713993010398,
-       "constrained":0.1233480139851019
-      },
-     "Rat":{
-       "original name":"Rat",
-       "Nucleotide GTR":0.06669700444436912,
-       "MG94xREV with separate rates for branch sets":0.0670850471739789,
-       "unconstrained":0.07366345007817726,
-       "constrained":0.06713082546371778
+       "unconstrained":0.04942545223877414
       },
      "Node1":{
-       "Nucleotide GTR":0.276880831396131,
-       "MG94xREV with separate rates for branch sets":0.2843521449765504,
-       "unconstrained":0.459085769955035,
-       "constrained":0.3115534692518958
+       "MG94xREV with separate rates for branch sets":0.2837967450491412,
+       "Nucleotide GTR":0.2767871391397028,
+       "constrained":0.1295742765519239,
+       "unconstrained":0.1515367890887531
       },
      "Node12":{
-       "Nucleotide GTR":0.01783434870161725,
-       "MG94xREV with separate rates for branch sets":0.01788794906051452,
-       "unconstrained":0.01828498503175797,
-       "constrained":0.01770410398930177
+       "MG94xREV with separate rates for branch sets":0.01788296579298991,
+       "Nucleotide GTR":0.01784443144961206,
+       "constrained":0.005338125135456628,
+       "unconstrained":0.00572208893382143
       },
      "Node2":{
-       "Nucleotide GTR":0.06617535490721377,
-       "MG94xREV with separate rates for branch sets":0.06447679597474805,
-       "unconstrained":0.0623969317369398,
-       "constrained":0.06097949807503514
+       "MG94xREV with separate rates for branch sets":0.06423714540466627,
+       "Nucleotide GTR":0.06616183769400197,
+       "constrained":0.02253286838656328,
+       "unconstrained":0.02248978054488407
       },
      "Node3":{
-       "Nucleotide GTR":0.09884524766349881,
-       "MG94xREV with separate rates for branch sets":0.1017497956116402,
-       "unconstrained":0.1285021744856729,
-       "constrained":0.1065011238088613
+       "MG94xREV with separate rates for branch sets":0.1017201477652066,
+       "Nucleotide GTR":0.09890202668045614,
+       "constrained":0.04280347934583096,
+       "unconstrained":0.04618990784049085
       },
      "Node8":{
-       "Nucleotide GTR":0.1061610073141143,
-       "MG94xREV with separate rates for branch sets":0.1093806684969149,
-       "unconstrained":0.1348034716617685,
-       "constrained":0.1118205234697939
+       "MG94xREV with separate rates for branch sets":0.1096720572321177,
+       "Nucleotide GTR":0.10624077635158,
+       "constrained":0.04415239867414091,
+       "unconstrained":0.04768889036449767
       },
      "Node9":{
-       "Nucleotide GTR":0.02568007351415409,
-       "MG94xREV with separate rates for branch sets":0.02593963430985144,
-       "unconstrained":0.02761127562964508,
-       "constrained":0.02639493109700932
+       "MG94xREV with separate rates for branch sets":0.02591275475412757,
+       "Nucleotide GTR":0.02566524291670843,
+       "constrained":0.00997308939110993,
+       "unconstrained":0.009841415288506062
+      },
+     "Pig":{
+       "MG94xREV with separate rates for branch sets":0.1928073761020463,
+       "Nucleotide GTR":0.1871746592118726,
+       "constrained":0.07816490289585476,
+       "original name":"Pig",
+       "unconstrained":0.08275992348314189
+      },
+     "Rat":{
+       "MG94xREV with separate rates for branch sets":0.06698958986289986,
+       "Nucleotide GTR":0.06656862018951525,
+       "constrained":0.02277034233250765,
+       "original name":"Rat",
+       "unconstrained":0.02372534359054489
+      },
+     "RhMonkey":{
+       "MG94xREV with separate rates for branch sets":0.003717482368324115,
+       "Nucleotide GTR":0.003775504255522691,
+       "constrained":0.001359450941376631,
+       "original name":"RhMonkey",
+       "unconstrained":0.00132482447204072
       }
     },
    "attributes":{
-     "original name":{
-       "attribute type":"node label",
-       "display order":0
-      },
-     "Nucleotide GTR":{
-       "attribute type":"branch length",
-       "display order":0
-      },
      "MG94xREV with separate rates for branch sets":{
        "attribute type":"branch length",
        "display order":1
       },
-     "unconstrained":{
+     "Nucleotide GTR":{
        "attribute type":"branch length",
        "display order":0
       },
      "constrained":{
        "attribute type":"branch length",
        "display order":1
+      },
+     "original name":{
+       "attribute type":"node label",
+       "display order":0
+      },
+     "unconstrained":{
+       "attribute type":"branch length",
+       "display order":0
       }
     }
   },
+ "data partitions":{
+   "0":{
+     "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] 
+      ],
+     "name":"busted.filter.default"
+    }
+  },
+ "fits":{
+   "Constrained model":{
+     "AIC-c":6918.851822592964,
+     "Log Likelihood":-3419.573452280089,
+     "Rate Distributions":{
+       "Synonymous site-to-site rates":{
+         "0":{
+           "proportion":0.3289898788632067,
+           "rate":0.3124849036133048
+          },
+         "1":{
+           "proportion":0.5748197734913485,
+           "rate":1.039520868895482
+          },
+         "2":{
+           "proportion":0.09619034764544485,
+           "rate":3.115265578623139
+          }
+        },
+       "Test":{
+         "0":{
+           "omega":0,
+           "proportion":0.02093092071081848
+          },
+         "1":{
+           "omega":0,
+           "proportion":0.1387433808480476
+          },
+         "2":{
+           "omega":1,
+           "proportion":0.8403256984411339
+          }
+        }
+      },
+     "display order":3,
+     "estimated parameters":39
+    },
+   "MG94xREV with separate rates for branch sets":{
+     "AIC-c":6997.089050462658,
+     "Equilibrium frequencies":      [
+[0.04875339327772683],
+      [0.03982858547830345],
+      [0.04946803524790992],
+      [0.04152216138298744],
+      [0.01811683453600613],
+      [0.01480036248560469],
+      [0.0183823965708893],
+      [0.01542969784826435],
+      [0.01894694796506697],
+      [0.01547851515238824],
+      [0.01922467805342367],
+      [0.01613668666381816],
+      [0.02832099415740372],
+      [0.02313654621336914],
+      [0.02873613184734657],
+      [0.02412034959764736],
+      [0.01662182431200483],
+      [0.01357902918971745],
+      [0.01686547203528639],
+      [0.01415643148428886],
+      [0.006176695005242439],
+      [0.005045987744654046],
+      [0.006267234867003878],
+      [0.005260551308914496],
+      [0.006459711194459957],
+      [0.005277194922783805],
+      [0.006554399593040238],
+      [0.005501589790395056],
+      [0.009655668202293983],
+      [0.007888099278638223],
+      [0.009797203904398108],
+      [0.008223514024394991],
+      [0.03326722643528176],
+      [0.02717732003095303],
+      [0.03375486749252685],
+      [0.02833294365668738],
+      [0.01236215156074466],
+      [0.01009913314808799],
+      [0.01254335971371867],
+      [0.01052856463184265],
+      [0.01292858539344675],
+      [0.0105618754683007],
+      [0.0131180965046964],
+      [0.01101098350431497],
+      [0.0193250328267319],
+      [0.01578738770911659],
+      [0.0196083049972345],
+      [0.01645869298147252],
+      [0.01962343746171723],
+      [0.02045785777700414],
+      [0.008926115885166477],
+      [0.007292098982657142],
+      [0.009056957588961733],
+      [0.007602170831388156],
+      [0.007626222986467745],
+      [0.009471947420992787],
+      [0.007950502328516303],
+      [0.01395367801862353],
+      [0.01139931439306339],
+      [0.01415821524731906],
+      [0.01188403168729233] 
+      ],
+     "Log Likelihood":-3467.004808147542,
+     "Rate Distributions":{
+       "non-synonymous/synonymous rate ratio for *test*":        [
+[0.9950576192409499, 1] 
+        ]
+      },
+     "display order":1,
+     "estimated parameters":31
+    },
+   "Nucleotide GTR":{
+     "AIC-c":7112.85745601076,
+     "Equilibrium frequencies":      [
+[0.3592490842490842],
+      [0.181959706959707],
+      [0.240018315018315],
+      [0.2187728937728937] 
+      ],
+     "Log Likelihood":-3532.321297387654,
+     "Rate Distributions":{
+       "Substitution rate from nucleotide A to nucleotide C":0.5497129763145497,
+       "Substitution rate from nucleotide A to nucleotide G":1,
+       "Substitution rate from nucleotide A to nucleotide T":0.264666902964203,
+       "Substitution rate from nucleotide C to nucleotide G":0.4916303643305098,
+       "Substitution rate from nucleotide C to nucleotide T":1.027924764411573,
+       "Substitution rate from nucleotide G to nucleotide T":0.304615404570875
+      },
+     "display order":0,
+     "estimated parameters":24
+    },
+   "Unconstrained model":{
+     "AIC-c":6910.766610587704,
+     "Log Likelihood":-3414.486640449675,
+     "Rate Distributions":{
+       "Synonymous site-to-site rates":{
+         "0":{
+           "proportion":0.2645541257391169,
+           "rate":0.2747941124675511
+          },
+         "1":{
+           "proportion":0.6325830460054784,
+           "rate":0.9734675888351726
+          },
+         "2":{
+           "proportion":0.1028628282554047,
+           "rate":3.028333913894314
+          }
+        },
+       "Test":{
+         "0":{
+           "omega":0,
+           "proportion":0.04809457608200497
+          },
+         "1":{
+           "omega":0,
+           "proportion":0.3410012743721951
+          },
+         "2":{
+           "omega":1.89363684081788,
+           "proportion":0.6109041495458
+          }
+        }
+      },
+     "display order":2,
+     "estimated parameters":40
+    }
+  },
+ "input":{
+   "file name":"/tmp/tmp7qHfo2/job_working_directory/000/3/working/./busted_input.fa",
+   "number of sequences":10,
+   "number of sites":187,
+   "partition count":1,
+   "trees":{
+     "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)"
+    }
+  },
  "test results":{
-   "LRT":44.77492170961614,
-   "p-value":1.893429857346973e-10
+   "LRT":10.17362366082671,
+   "p-value":0.003088842014430382
+  },
+ "tested":{
+   "0":{
+     "Baboon":"test",
+     "Cat":"test",
+     "Chimp":"test",
+     "Cow":"test",
+     "Horse":"test",
+     "Human":"test",
+     "Mouse":"test",
+     "Node1":"test",
+     "Node12":"test",
+     "Node2":"test",
+     "Node3":"test",
+     "Node8":"test",
+     "Node9":"test",
+     "Pig":"test",
+     "Rat":"test",
+     "RhMonkey":"test"
+    }
+  },
+ "timers":{
+   "Constrained BUSTED model fitting":{
+     "order":3,
+     "timer":62
+    },
+   "Overall":{
+     "order":0,
+     "timer":228
+    },
+   "Preliminary model fitting":{
+     "order":1,
+     "timer":3
+    },
+   "Unconstrained BUSTED model fitting":{
+     "order":2,
+     "timer":161
+    }
   }
 }
\ No newline at end of file