annotate test-data/busted-out1.json @ 3:70aa4bada58d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 16da4cfb8e771ea5e7dc2772c4fe2c160535838b"

{
 "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] 
    ]
  },
 "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":"[e-mail]",
   "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,
 "branch attributes":{
   "0":{
     "Baboon":{
       "MG94xREV with separate rates for branch sets":0.001771850913718116,
       "Nucleotide GTR":0.00167976779100812,
       "constrained":0.0005055252388761481,
       "original name":"Baboon",
       "unconstrained":0.0005398732671668005
      },
     "Cat":{
       "MG94xREV with separate rates for branch sets":0.2738959056554072,
       "Nucleotide GTR":0.266075486389923,
       "constrained":0.1152712488116292,
       "original name":"Cat",
       "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",
       "unconstrained":0.04942545223877414
      },
     "Node1":{
       "MG94xREV with separate rates for branch sets":0.2837967450491412,
       "Nucleotide GTR":0.2767871391397028,
       "constrained":0.1295742765519239,
       "unconstrained":0.1515367890887531
      },
     "Node12":{
       "MG94xREV with separate rates for branch sets":0.01788296579298991,
       "Nucleotide GTR":0.01784443144961206,
       "constrained":0.005338125135456628,
       "unconstrained":0.00572208893382143
      },
     "Node2":{
       "MG94xREV with separate rates for branch sets":0.06423714540466627,
       "Nucleotide GTR":0.06616183769400197,
       "constrained":0.02253286838656328,
       "unconstrained":0.02248978054488407
      },
     "Node3":{
       "MG94xREV with separate rates for branch sets":0.1017201477652066,
       "Nucleotide GTR":0.09890202668045614,
       "constrained":0.04280347934583096,
       "unconstrained":0.04618990784049085
      },
     "Node8":{
       "MG94xREV with separate rates for branch sets":0.1096720572321177,
       "Nucleotide GTR":0.10624077635158,
       "constrained":0.04415239867414091,
       "unconstrained":0.04768889036449767
      },
     "Node9":{
       "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":{
     "MG94xREV with separate rates for branch sets":{
       "attribute type":"branch length",
       "display order":1
      },
     "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":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
    }
  }
}