view test-data/busted-out1.json @ 27:8c388fd08c09 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2063bc1f8f9cb97de147b86dbe9189fc496b206a"
author iuc
date Wed, 09 Jun 2021 17:34:05 +0000
parents 1fb98a84e86d
children
line wrap: on
line source

{
 "Evidence Ratios":{
   "constrained":    [
[1.751697313438667, 0.9490151622254345, 0.9575938099872893, 1.827482077500528, 1.505094606485015, 2.088346790071941, 7.070051504373732, 3.867967952992799, 2.545750919582881, 0.7247660693488289, 0.3196737937441124, 1.489449650902744, 0.6530151351740718, 1.04337285373284, 1.058333334239147, 0.5088801718500566, 0.8550055907613735, 1.110381942461004, 0.565683766000719, 0.6740763008813015, 0.4649952970969699, 0.4036426325687712, 2.442336342315371, 0.9859501295040206, 1.104892115806872, 1.062417300927637, 1.753888646580218, 1.31233150141181, 1.885518048500539, 0.7894296553774935, 0.723576644239061, 0.8827532839004689, 0.6984548336173313, 4.520258616283331, 0.501963856483453, 1.807812329244406, 0.6240669422720765, 0.9486848826066486, 0.9673516986934556, 1.479968294590536, 1.364799619489093, 1.709865961585205, 1.218557239747954, 0.7108467425303473, 0.3215450048962207, 2.271412336163041, 0.6355183534074139, 0.8839058954441763, 1.497501825835906, 2.637709102972778, 1.711470421506773, 3.027431470913309, 1.57278424917318, 3.277990564747366, 6.926286311855851, 3.784092751645639, 3.146955337815139, 1.955427417762355, 2.022694964562529, 0.666396825353515, 3.560060598929708, 1.666971860419219, 1.738637096007019, 3.220829375167113, 0.3447106216301303, 0.4881402535027675, 1.387141991322175, 0.5556476307196163, 0.6310295884570762, 0.4580705327203016, 0.4272583872429177, 2.901848650844198, 0.9999999999999991, 1.027519028508734, 2.915165037860989, 2.8354880840935, 1.858569677080054, 0.4521292148676688, 3.009136246768449, 0.705314987368983, 2.743480940643173, 0.3932432097494273, 0.9370673501878248, 0.4620247121091633, 2.83829096947346, 0.9007779218604833, 0.3302046680129435, 1.07627096358673, 1.391320542790854, 1.521972158264955, 0.4323783230969274, 2.334048026570822, 2.149795581008433, 3.074008352247498, 0.4499660997382409, 1.699461664815503, 0.8463586773204229, 2.696688856522739, 0.5804226171984278, 1.135876829610681, 0.8103519829402507, 2.896966803514224, 0.8351241901463535, 1.602690102144888, 0.7282588483860968, 2.78698806913424, 0.9149220061406503, 0.6214951247464974, 1.819052515045006, 0.2353728426618933, 2.441495991316177, 0.4689975029575301, 6.36479070098702, 0.501963856483453, 1.155173566804371, 0.3029791752249296, 3.710694239289469, 0.7371667962152887, 1.911346283016054, 0.3691203298834842, 1.027711744192628, 1.502724363578014, 0.3011502503588185, 0.9854850481813123, 0.3756291290353144, 4.112619261559145, 2.95680467264194, 0.4290868700547413, 0.4685206821924932, 0.4059560116267469, 2.50268310954176, 0.5227540827634783, 0.4671119113495291, 0.9338453011500626, 0.5571522059019809, 0.5886144003589358, 1.839204151926823, 1.060599026952742, 3.125234562282934, 2.54439731915596, 5.066889740057174, 2.915048895304102, 1.905524097635808, 2.212264991895895, 3.738815510070657, 2.074128973780481, 3.31083714843465, 0.6408491718084866, 3.068722634962862, 0.9229478196348808, 2.172843296216792, 1.750529904876356, 1.222415748191823, 1.340180507105605, 1.65676234501901, 1.177884311452671, 1.853985207061093, 1.949028686126, 1.848056555892881, 1.490331787720329, 2.808897643683787, 0.5370047325763545, 0.754447735175597, 0.292920631250886, 1.922199953975427, 0.2194780669088011, 2.411432550287456, 0.4936742969382611, 2.687417056073211, 0.8937719293629136, 0.630203462304753, 3.500554848762429, 0.8047116371904648, 2.9258711565943, 2.978602987543041, 1.892870394871532, 1.224886235480212, 3.334368853761007, 1.443700495825233, 1.7051887541283, 0.480593393899601, 0.907604501104216, 0.9198540076829841, 0.8702783448030316, 0.4699917745647508, 0.6213048344098008, 0.9960464828596589] 
    ],
   "optimized null":    [
[1.115754847329475, 0.9981043798375602, 0.9996678649277134, 1.027524895296611, 0.7950614097315224, 0.6815044886735678, 0.9660630441693723, 1.768207537367336, 1.995453831253169, 0.9376497008654193, 0.6553491413144868, 1.461081981960806, 1.013114798606584, 1.166859848568389, 0.6014901871758097, 0.8123191197415052, 0.9580261569974873, 1.198185908129791, 0.9405425950826685, 0.971114257615956, 0.9488537673129271, 0.8646610989285944, 0.7646430387003397, 0.9893117681890439, 1.197283659537823, 1.211007891429009, 1.187153808700299, 1.379812109844639, 0.9624959240764994, 0.7612299911652801, 0.7835844165719837, 0.885684857590916, 1.279101118649989, 0.7844909969836256, 0.9105640059139158, 0.987661389211442, 0.7933470171962204, 1.000355360146534, 1.004491368971939, 1.287636006929032, 1.025334362891704, 0.8161200204209572, 1.800919746565827, 0.7201977656989363, 0.7006786063830531, 0.8445748286055409, 1.13557449720856, 0.9408284217407435, 0.8291599938547976, 0.7847367003613621, 0.6044458050342899, 0.8578237870323223, 1.028327328223754, 3.732522507488938, 1.284572434603426, 0.9117994273854937, 1.151534378021883, 1.002963004237252, 0.9184071418215726, 0.8891548248386872, 1.107752217118886, 1.08471556447794, 0.904519273163679, 0.9915866239749839, 0.8379284266222653, 1.039306992564055, 1.699720775349538, 0.9164148538876519, 1.031865543996781, 0.8814594623715953, 0.8357649706134436, 1.211073491981048, 0.9999999999999991, 1.09042273536382, 0.8969295321069349, 2.282699983096541, 0.6906271160345826, 1.004025552082599, 1.229544542202273, 1.020229958793708, 1.635583530470503, 0.9012757793992182, 0.9262513777205981, 0.755045001493049, 0.5956960416334989, 0.6446026033796701, 0.7494241039808305, 1.081919574928575, 0.736166264060359, 1.130809144056797, 0.9190054297705696, 1.465760638675436, 1.264811511728797, 1.077114430307984, 0.9731626619098518, 1.046507786460218, 1.038574549189271, 1.434108431082798, 0.9595323092739115, 1.311940940446743, 1.010601751735099, 1.484849122531978, 0.9467219554462175, 0.9999147957468079, 0.9337530742390975, 1.014803716779695, 1.007462002443472, 1.01533333078764, 1.148263019382676, 0.7422032808770405, 0.8639145321361502, 0.8673930454219201, 2.026916851640757, 0.9105640059139158, 0.7803929380437222, 0.8703888058550368, 1.410247919613535, 0.9914652054039267, 0.7814313499738406, 0.7431099613737392, 1.113679671632678, 1.531754344457596, 0.7916210828345887, 0.7180922698986317, 0.8040633094792566, 1.035367687704656, 1.108843159118376, 0.8485144325155356, 0.9245149419204511, 0.9856066046472061, 2.840752049492474, 0.9719349042983756, 0.9513072209812393, 0.9818577734913401, 0.8190574737799189, 0.7957337116895524, 1.058600036393583, 1.378130836062728, 1.543996499685658, 0.9157765463527018, 1.371864786157317, 1.179088778643788, 0.8990667969958885, 0.8491807688030968, 1.430795716876661, 0.8233279102457327, 1.602054722411324, 0.9947248981278961, 1.450547523094791, 0.8328149332184142, 1.865584692965049, 1.606267608729814, 0.7854775725228893, 1.235086019516011, 0.8715583188734622, 0.9003125968429074, 0.8577816502175432, 1.466928944424435, 0.7382231658168724, 1.118381528668526, 1.062150053798357, 0.8645443140611492, 0.8866230937072818, 0.8323827468669284, 1.495223917742498, 0.8220538187834464, 1.189868122430675, 0.9871334636897435, 0.7944859535178556, 1.0925978798477, 1.52803476753022, 1.276753099905758, 1.069980901551178, 1.586787129488837, 2.015280193477939, 1.124546923383764, 0.8906149060472343, 0.9027629088385779, 1.472050188194838, 0.6332413644351131, 0.9451405108005444, 0.8291877249363551, 0.9274410423803646, 0.9465758585718032, 1.007518685935051, 1.117050744578768, 1.604376953048971] 
    ]
  },
 "Site Log Likelihood":{
   "constrained":    [
[-10.45090262193947, -3.483902519448886, -3.812918674840162, -18.52967367048658, -17.91293552421441, -29.82234031390563, -32.4682953322895, -26.13136592613271, -18.98353837196509, -10.33536376131518, -16.46521792962993, -23.85656647453301, -20.0097735066148, -16.65014379412616, -21.98016668059303, -12.27360074288172, -10.6941140816234, -15.60391557669279, -11.01584022727405, -8.52552567646616, -8.213958972448863, -11.44408858234599, -24.88483689931558, -13.63702466513553, -14.85783877857095, -14.70130071011686, -22.04314741356357, -15.9841391162467, -21.7894026756885, -18.56582389265503, -22.2970319079228, -14.20013718887272, -10.46062459593404, -29.63172583834114, -5.942895596547681, -33.7608698289049, -15.4453605547865, -4.280368277884408, -4.808122799169091, -24.62846286067449, -19.95038043810364, -20.73996670837995, -12.75582605885885, -18.99209486958509, -14.29899136245764, -24.5323131442472, -16.76719624729421, -15.30050374515202, -21.1470077553502, -23.70452335151525, -28.92097938243611, -31.11127051701743, -20.64056509230148, -24.08245503901272, -32.37575293948952, -27.1397706688597, -28.48714117432097, -21.8157658433444, -23.86066380099029, -15.96179451261716, -22.90078930509975, -22.82780054877238, -18.85863915537205, -24.13596526976866, -13.11062461592573, -6.997019061890909, -20.27078018556115, -11.63234308244865, -10.76772040073618, -9.375030039476741, -8.838080080197956, -22.23813284474415, -5.071925291421929, -11.59502858303457, -24.88722835704511, -26.44848697533541, -29.47226045522432, -14.40683310705516, -30.18120324933559, -15.08227050749874, -24.4722144291366, -9.970786483716564, -12.02451510684466, -10.47801146285196, -32.58390043458385, -22.41272747457295, -15.45732063757284, -18.58799241229831, -24.88853139164258, -16.45692685905665, -9.360428939345834, -21.91694140733639, -23.88498099910663, -25.3962161614738, -13.12135916900047, -23.54673109739056, -13.53887882815504, -25.35896009046736, -12.94299852184595, -18.79824781975578, -14.2386090251928, -22.25439432796464, -10.55845974254318, -21.47824043379306, -10.39206663293596, -24.52508757095106, -11.36803395343945, -6.913098566554392, -21.83429025783947, -17.94930007893821, -24.44667277945298, -8.760710459872854, -25.49076161826261, -5.942895596547681, -26.74335661856266, -11.95479247264214, -26.11935275663087, -8.84576691015538, -22.23961500868496, -12.65473600559412, -11.95172286310796, -16.44673955121138, -12.22327296206971, -19.44139078647339, -12.04821884318743, -26.74230137861179, -24.26902923541198, -10.42122278454815, -18.05639580573808, -12.67270476859209, -24.89079815344573, -13.28852575517897, -12.15758680881002, -15.22362700005587, -11.1087132369094, -15.26580355619412, -21.1714116232631, -17.44878592939348, -22.90508349789376, -32.10916540506811, -34.70167299760255, -29.45222601783585, -23.82489796368972, -25.17657127603625, -26.14089446397534, -28.36631233203936, -24.37577873996561, -11.83810875252699, -22.98051281763511, -14.10620053901725, -27.43594024958254, -16.95410198934557, -16.47464786440968, -16.5154876564325, -17.6698746836033, -14.75877758237345, -19.62594140417327, -21.72627428789965, -27.06861465296137, -23.30295590843949, -30.34866123718632, -14.39953916526644, -9.002852170879979, -13.04044047087386, -22.59571981707717, -16.84927191220984, -27.56793378022781, -5.44310980584226, -29.46507972190871, -10.76293375912305, -14.40381349426134, -21.63861962597842, -13.81954299123125, -26.27612327461895, -25.94071651096489, -30.30727965502338, -18.73706186163648, -29.88139839294296, -18.59623366674176, -26.60843026312014, -7.063609265673095, -20.10755427375394, -13.68702804353427, -13.85651640481543, -7.108876310942952, -7.279280331780171, -20.4371936150988] 
    ],
   "optimized null":    [
[-9.999848579629438, -3.534335603769343, -3.855918073448204, -17.9538874611, -17.2747438441717, -28.70251512907133, -30.47790138370519, -25.34860297645322, -18.73998421748136, -10.59289124751458, -17.18308498211639, -23.83733702940499, -20.44895802290328, -16.76200145058928, -21.41512627843794, -12.74128144037208, -10.80788115515916, -15.68002019797957, -11.52426196006769, -8.890626497321907, -8.927186376073541, -12.20589630571461, -23.72353563066267, -13.64042840813737, -14.93814645500984, -14.83220690675711, -21.65287069195306, -16.03428112649423, -21.11697461820088, -18.52944869764263, -22.37670423099836, -14.20345263011663, -11.06566694045806, -27.88043644714669, -6.538431672725973, -33.15633700907163, -15.68536363930423, -4.333402162466966, -4.845797260874019, -24.48925018012824, -19.66439158624725, -20.00035787499095, -13.14645599501158, -19.00516386388902, -15.07790314758396, -23.54298939203635, -17.34764924361699, -15.36291392817002, -20.55586733882526, -22.49220554409181, -27.88018322030692, -29.85019937935898, -20.21565116547379, -24.21230871760245, -30.69085508292206, -25.71662926722871, -27.4818010431507, -21.14811566898335, -23.0711185608064, -16.25018056217564, -21.73334467076629, -22.39810962558813, -18.20518596093719, -22.95787740520259, -13.99885201582488, -7.752725709331387, -20.4739986642663, -12.13267790621028, -11.25949129864883, -10.02958587932763, -9.509038565562101, -21.36429199478783, -5.071925291421929, -11.65444684825109, -23.70852394255006, -26.23163183473617, -28.48229802380226, -15.20463784468526, -29.28619398287981, -15.45140934453945, -23.95498653878558, -10.80016950117357, -12.01290561268065, -10.96917043588625, -31.02267359559108, -22.0781027350932, -16.27691301947574, -18.59322700501767, -24.25197878119941, -16.15985332581128, -10.11442001712052, -21.45171161176134, -23.35453134857961, -24.34751944095499, -13.89273816685505, -23.06187826758802, -13.74354001612338, -24.72747877321687, -13.44568802121267, -18.94235060457898, -14.45944155129241, -21.58604323426556, -10.68388474245953, -21.00647169464934, -10.64062211576559, -23.51482131466939, -11.46438470940085, -7.403942742248016, -21.37422487105309, -19.09775242663159, -23.40778038061878, -9.375605229265306, -24.34649611581681, -6.538431672725973, -26.35114829216582, -13.01006841322404, -25.15189928947141, -9.142136580235025, -21.34517917780335, -13.35445734769922, -12.03205769212679, -16.46587355698196, -13.18974649780325, -19.12485490220534, -12.80929455473056, -25.36299788062012, -23.2882373255091, -11.10305048579558, -18.73608477233943, -13.55971725450759, -25.01750357654675, -13.9087034380676, -12.86885500181513, -15.2737626703588, -11.49402903111002, -15.5672968520748, -20.61902598615607, -17.71068017555166, -22.19994834214875, -31.08728870377415, -33.39511680382837, -28.5470813431575, -23.07374293025032, -24.21907120646889, -25.18035634613069, -27.44237031336156, -23.64986467449063, -12.27778083932105, -22.23119250973097, -14.00343928803062, -27.28347817719133, -16.86809667669382, -16.0323554685095, -16.43382396383096, -17.02753688184933, -14.49004446342468, -18.85519821718548, -21.44211421111342, -26.15097096898469, -23.01583971345514, -29.37616433486512, -14.87573482137308, -9.16428613534381, -14.0848311489858, -22.34452545099508, -18.16982547353947, -26.86155526961141, -6.13603907590076, -28.24643921897574, -10.96379664456025, -15.28950849406241, -20.63001835633828, -14.10445507093618, -25.66424230560382, -25.5500203560601, -29.78656547037373, -18.41837074179778, -28.57481966126671, -18.61568017561408, -25.61785082518842, -7.739921293110954, -20.01719213846289, -13.69524229967891, -13.94055442162264, -7.871406957800698, -7.865905721003565, -20.91389045801702] 
    ],
   "unconstrained":    [
[-9.890317410653219, -3.536233022893474, -3.85625026368956, -17.92673456500613, -17.50407976653743, -29.08596757047699, -30.51242756748906, -24.77863663373813, -18.04911270867274, -10.65727010047667, -17.60567212730394, -23.45815978461676, -20.43592847868088, -16.60768519998243, -21.9234713360606, -12.94914345179085, -10.85076135278797, -15.49921152824752, -11.5855603015069, -8.919937644887968, -8.979686959664745, -12.35131394768199, -23.99188180079542, -13.6511741693905, -14.75809108112158, -14.64075392575073, -21.48131200704493, -15.71233378888117, -21.15520006575576, -18.80226844212963, -22.62058071107572, -14.32484671297345, -10.81950936027501, -28.12315663014189, -6.63212275746709, -33.16875237251921, -15.91685819187105, -4.333046865445894, -4.841315948000512, -24.23644219570189, -19.63937281915182, -20.20355172597554, -12.55815849029599, -19.33339329399536, -15.43360912343386, -23.71191133170305, -17.22051055580043, -15.4239084202805, -20.74320948508744, -22.73461257510765, -28.38362648580198, -30.00355595636499, -20.18771763645436, -22.89522443705173, -30.44042915566087, -25.80896450643621, -27.34070574832697, -21.14515704579125, -23.1562330378798, -16.36766446463329, -21.63101173820942, -22.31679182551859, -18.30553762722511, -22.96632637345011, -14.17567460773119, -7.714171571593938, -19.94353467648899, -12.21996402578803, -11.22812292690234, -10.15576214462901, -9.688446406615418, -21.1727848450384, -5.071925291421929, -11.56788139658788, -23.8173019220834, -25.40627288927275, -28.85245325414149, -15.2006203734581, -29.07955017296254, -15.4313812928555, -23.46298689873945, -10.90411348791657, -12.08951522763595, -11.25014836276909, -31.54069833485993, -22.51722400594995, -16.56536324824294, -18.51449015736655, -24.55827806470882, -16.03691989264587, -10.19888326541777, -21.06933729674679, -23.11960824008805, -24.27323379929944, -13.91994220197101, -23.0164195642338, -13.70569086891633, -24.36693541947492, -13.48699731228228, -18.67084292997368, -14.44889560405677, -21.19073006816119, -10.73863457701958, -21.00655690253262, -10.70916536594832, -23.5001261033595, -11.45695040996968, -7.388725778950405, -21.2359744884371, -19.39588453652134, -23.5540618168286, -9.517868294607256, -23.63998026959247, -6.63212275746709, -26.59910601158946, -13.14888367710742, -24.80813377102439, -9.150708004758682, -21.59180715470589, -13.65136859644867, -11.92438813987756, -16.03945984809169, -13.42341893021988, -19.45601211078778, -13.02737182450041, -25.32824126316957, -23.18492005264431, -11.26731867080138, -18.81457083846118, -13.57421523958925, -23.97343475326927, -13.93716988571839, -12.91877321996798, -15.29207148498773, -11.69363005314582, -15.79578753423454, -20.56207867133534, -17.38995206112281, -21.76557415759171, -31.17527159287139, -33.07894583174475, -28.38233942448484, -23.18014087607957, -24.38255440213001, -24.8221256112489, -27.63677103815755, -23.17857766761929, -12.28306990366699, -21.85925142243789, -14.18638311853461, -26.65990366493676, -16.39418344445917, -16.27381884205222, -16.2226833447466, -17.16500938029794, -14.5950577095621, -19.00860391599289, -21.0589431491008, -26.45448007637202, -22.90395713694845, -29.31586912843093, -15.0212875367872, -9.284621444861237, -14.26829406063716, -21.94224947761382, -18.36577488663612, -26.68771279011595, -6.148989103020872, -28.47649919178767, -10.87523840804787, -14.86552604995768, -20.38569814182948, -14.03681427163925, -25.20253100696378, -24.84926211649333, -29.66918525060677, -18.53421389094812, -28.67711498073234, -18.22902406064756, -26.07475445227853, -7.796342966974589, -20.20450084049472, -13.77056835236659, -13.99545858676251, -7.86391639630019, -7.755213772603022, -20.44115496804752] 
    ]
  },
 "Synonymous site-posteriors":  [
[0.6590420682141636, 0.6295262952117998, 0.6303856865370306, 0.7651708815907992, 0.8822084774809541, 0.6463878945255449, 0.05670925821127412, 0.9065880565181345, 0.8313877625727055, 0.5008097537233324, 0.3827028155918334, 0.8741668571674565, 0.6785611443171407, 0.6592269988543858, 0.8934109043144369, 0.2898485544301485, 0.1752690860478696, 0.5237553031185891, 0.1438583959125483, 0.1310481754808935, 0.2782000142626717, 0.1326603115533762, 0.9202844322281382, 0.4423979179896382, 0.4479578734222657, 0.8331602216928046, 0.925163725370258, 0.7381010022271582, 0.8760396800736433, 0.9007107726896093, 0.8616719133142033, 0.429318638666869, 0.427221193776739, 0.9646106201610571, 0.2521158347717649, 0.08679404343699054, 0.8791675458832844, 0.629151430043082, 0.6309399626011464, 0.7773892793695361, 0.911747762174925, 0.8406524716876108, 0.5384380892981991, 0.9355402336009301, 0.3834858892943144, 0.8056298368250397, 0.8976220110421324, 0.7877202353863311, 0.8919996668839869, 0.919705598959816, 0.3525779358136313, 0.1806859168593065, 0.7335566438646067, 0.6837189356889364, 0.1887528496215639, 0.7930815508520332, 0.1064227299060983, 0.8862924753363561, 0.9370309940701347, 0.8646550974880528, 0.8790909163593805, 0.8334691601726457, 0.8090002820495114, 0.9493479317981891, 0.643279137499093, 0.04082058885229868, 0.8658866867002749, 0.160001761068033, 0.5542784925796955, 0.3412581912517945, 0.3915136973392245, 0.9289484814870412, 0.6321791898264182, 0.1215195300290875, 0.7545656400684584, 0.8987389979543963, 0.4741316117530976, 0.7694841080735656, 0.1503068855058662, 0.527100842548382, 0.8538952483000255, 0.7010382439666797, 0.4675076722121743, 0.2219386697671104, 0.0673963342718981, 0.916001585621829, 0.851572145102629, 0.8697783185834219, 0.9093904942772238, 0.8122276217738864, 0.1302818240907984, 0.8532983433628731, 0.8681669010866113, 0.925606685349572, 0.5332251731370758, 0.8326655111978812, 0.7636853657679995, 0.9166475703028997, 0.5177756387836665, 0.8929964503319083, 0.5684339147070099, 0.9346722912515401, 0.253062138148439, 0.8907895575117083, 0.2217508534552121, 0.902154690335745, 0.1255139411661346, 0.09284933655314186, 0.8854084148486325, 0.6591556884674684, 0.6311072237304626, 0.2275766794873746, 0.9698271069023099, 0.2521158347717649, 0.5797595970139706, 0.5159911744822987, 0.9264165580831163, 0.2064195936853306, 0.9351559780006461, 0.3618435718977148, 0.1476766883148213, 0.4643540168121424, 0.5299736797978728, 0.859593764540069, 0.4684915458291029, 0.8960255042184201, 0.791713911497042, 0.1407003329894658, 0.7970189537714087, 0.7264738512114783, 0.9572821678630518, 0.8206779898514492, 0.6048512888727763, 0.7848399280841521, 0.1354695705305201, 0.876512495275497, 0.9037407480457214, 0.9086423009749222, 0.9481679440397182, 0.2817024062858178, 0.3391850707553216, 0.9483975919621521, 0.8327579573392221, 0.5363393536531582, 0.9386144376156097, 0.9625243792623214, 0.9585332162064392, 0.5728399516322858, 0.908818065422233, 0.3460193016854158, 0.7147896212869103, 0.8413769024552699, 0.6332901745005061, 0.8731249413033565, 0.897415228319015, 0.2375555670442387, 0.8911247286857046, 0.9250752271724603, 0.7129647593506242, 0.9522882419163263, 0.608915685087283, 0.5539252055276097, 0.244585468659001, 0.5218228361825763, 0.8651698499508601, 0.8546403232680236, 0.4567005108355059, 0.08986346650023433, 0.5309401738889369, 0.1119994110349295, 0.6793255623714524, 0.9367017183901303, 0.7398006182861786, 0.9254944521997526, 0.8914543038239114, 0.5915451341046691, 0.8828230293771862, 0.8253644148278831, 0.8818849284868315, 0.8469122381742665, 0.07842884343421058, 0.7347338880160806, 0.4273250135054775, 0.7729749543377356, 0.0441287679444981, 0.03939360753340206, 0.913447436171324],
  [0.2548059128700653, 0.07575394180863826, 0.07841949610132874, 0.2183464962709025, 0.1006670759949091, 0.3532824486382332, 0.9432883712267999, 0.08992863388772611, 0.001974472834862997, 0.004693076713445249, 0.001541968400693699, 0.001906321637908711, 0.002067575829753574, 0.00277290738529337, 0.01061698837402555, 0.0007205145207030305, 0.0001106812552033643, 0.004194917695983845, 4.785648754161972e-05, 0.0001649795194617654, 0.0006385642594312933, 0.0001343596935877354, 0.07298534944525173, 0.0005142400827715665, 0.001033196057862116, 0.05443053130322333, 0.0110279017015023, 0.006295099828154693, 0.1114827388456945, 0.03464971093576047, 0.07148060525787228, 0.001826796216604849, 0.00115176751565306, 0.01826368404588752, 0.00146700810621202, 0.9132016262738031, 0.01487306905206791, 0.07350227892135838, 0.07924660568572314, 0.220448971120644, 0.07921591222230702, 0.02325115413105475, 0.002338365525084445, 0.03390933129962609, 0.001924569061516209, 0.1934359057193492, 0.05066433063901594, 0.009791168493266059, 0.0862360189071557, 0.07511822878668947, 0.647037069082898, 0.8192938839855993, 0.0009524952524965365, 0.3135108983306193, 0.8112041978408995, 0.2044657628960425, 0.893566918656112, 0.03661091936124507, 0.02018364167430978, 0.05510274371092211, 0.1110470336593714, 0.1625056864787209, 0.004220667036113341, 0.02449010906318826, 0.01420146105439874, 1.218239057009355e-05, 0.01217566565790062, 5.967256014800797e-05, 0.003377588823932065, 0.00144201790563899, 0.004106787320422196, 0.03409211571956682, 0.1023170939677617, 2.024940947348321e-05, 0.2401962030926485, 0.07465230914721981, 0.5255210916473219, 0.01430992878722106, 0.8496891988811796, 0.0008263657392074046, 0.003811994607524969, 0.009899762571679077, 0.001897163664766378, 0.0003895444412942559, 0.9326020754649009, 0.07332124086182071, 0.07876708381532721, 0.007593167507380162, 0.08109390902694207, 0.01150220284122374, 0.0001068954307611358, 0.1397126431020345, 0.116897243588615, 0.06373683228264838, 0.001477063473647544, 0.1603419073791432, 0.006252946692834623, 0.03822377101065472, 0.001564529597146644, 0.02630865621376109, 0.001937385068883362, 0.02344264926816365, 0.0003608048117606154, 0.00439652934760935, 0.0006132092840562507, 0.05609506471149763, 3.222975570899437e-05, 3.298447131704098e-05, 0.1071408275827107, 0.008389592920554495, 0.3658713419592576, 0.0003836644318942201, 0.0154418969896028, 0.00146700810621202, 0.4199566326828601, 0.005290779887023487, 0.005601165990336834, 0.0003465676054746508, 0.01695068770483135, 0.0007888334817280919, 4.019755297084685e-05, 0.000257233239696642, 0.00641016986370742, 0.01007947552395773, 0.001926194304301807, 0.0990579122227388, 0.2029715521525786, 0.0001534711152938896, 0.022853667173833, 0.009503019344917743, 0.02221715661078068, 0.02648623197833246, 0.002298513739015609, 0.0123015920280185, 3.62206489591339e-05, 0.03776177341422494, 0.009202034016170254, 0.03475226912293359, 0.03972671492314912, 0.7181840822596014, 0.6607229937135094, 0.02225500720744548, 0.1627674796251149, 0.4632296040490493, 0.05087234197325657, 0.008597944062751987, 0.02764264895090687, 0.005444288019734069, 0.002166915494793255, 0.0005652492294085686, 0.2844331023365414, 0.009716360525106502, 0.001933172785401054, 0.01916140342833262, 0.0498368157991825, 0.0001061400191817122, 0.01668105211625924, 0.02186219683342442, 0.286075737255138, 0.02957656482283962, 0.3906823731474425, 0.003646619369260028, 0.0006503201097074237, 0.006866695803878058, 0.128411385510635, 0.02529046263357605, 0.5431649595823219, 0.0001295968024717857, 0.4686242786669976, 2.457268967041805e-05, 0.006951097038262886, 0.040741109168412, 0.007231150071612593, 0.05161065858320939, 0.1015436964867685, 0.4072081440937386, 0.01471997957948087, 0.1727426049271184, 0.005170073067439303, 0.1499368842971476, 8.824447363230611e-05, 0.001225387797452016, 0.001859485148828998, 0.00973084716656689, 1.536928208044389e-05, 2.436480520943331e-06, 0.05762972409721398],
  [0.08615201891577115, 0.294719762979562, 0.2911948173616405, 0.01648262213829845, 0.01712444652413669, 0.0003296568362220048, 2.370561926018262e-06, 0.003483309594139364, 0.1666377645924315, 0.4944971695632224, 0.615755216007473, 0.1239268211946347, 0.3193712798531057, 0.3380000937603209, 0.09597210731153759, 0.7094309310491486, 0.8246202326969269, 0.4720497791854272, 0.8560937475999101, 0.8687868449996448, 0.721161421477897, 0.8672053287530361, 0.006730218326610161, 0.5570878419275902, 0.5510089305198722, 0.1124092470039721, 0.06380837292823981, 0.255603897944687, 0.01247758108066221, 0.06463951637463027, 0.06684748142792442, 0.5688545651165263, 0.571627038707608, 0.01712569579305543, 0.7464171571220229, 4.330289206334114e-06, 0.1059593850646479, 0.2973462910355595, 0.2898134317131303, 0.002161749509819791, 0.009036325602767977, 0.1360963741813345, 0.4592235451767165, 0.0305504350994439, 0.6145895416441695, 0.000934257455611137, 0.0517136583188517, 0.2024885961204029, 0.02176431420885732, 0.00517617225349442, 0.0003849951034706128, 2.019915509414192e-05, 0.2654908608828966, 0.002770165980444209, 4.295253753668126e-05, 0.002452686251924292, 1.035143778976878e-05, 0.07709660530239872, 0.04278536425555551, 0.08024215880102509, 0.009862049981248162, 0.004025153348633382, 0.1867790509143752, 0.02616195913862262, 0.3425194014465082, 0.9591672287571313, 0.1219376476418244, 0.839938566371819, 0.4423439185963724, 0.6572997908425664, 0.6043795153403534, 0.03695940279339195, 0.2655037162058199, 0.878460220561439, 0.00523815683889315, 0.02660869289838387, 0.0003472965995805571, 0.2162059631392134, 3.915612954198521e-06, 0.4720727917124106, 0.1422927570924497, 0.2890619934616412, 0.5305951641230594, 0.7776717857915953, 1.590263200947959e-06, 0.01067717351635039, 0.06966077108204383, 0.122628513909198, 0.009515596695834129, 0.1762701753848898, 0.8696112804784405, 0.006989013535092396, 0.01493585532477367, 0.01065648236777971, 0.4652977633892768, 0.0069925814229755, 0.2300616875391659, 0.04512865868644578, 0.4806598316191869, 0.08069489345433063, 0.4296287002241067, 0.04188505948029637, 0.7465770570398003, 0.1048139131406824, 0.7776359372607317, 0.04175024495275743, 0.8744538290781564, 0.9071176789755411, 0.007450757568656826, 0.3324547186119771, 0.00302143431027981, 0.7720396560807312, 0.01473099610808742, 0.7464171571220229, 0.0002837703031692917, 0.4787180456306779, 0.06798227592654692, 0.7932338387091947, 0.04789333429452255, 0.6373675946205571, 0.8522831141322078, 0.5353887499481609, 0.4636161503384199, 0.1303267599359733, 0.5295822598665952, 0.004916583558841202, 0.00531453635037949, 0.8591461958952403, 0.1801273790547582, 0.2640231294436038, 0.02050067552616764, 0.1528357781702183, 0.3928501973882081, 0.2028584798878294, 0.8644942088205207, 0.08572573131027804, 0.08705721793810832, 0.05660542990214418, 0.01210534103713276, 0.0001135114545804652, 9.193553116902996e-05, 0.02934740083040224, 0.004474563035662842, 0.0004310422977926142, 0.01051322041113382, 0.0288776766749267, 0.01382413484265393, 0.4217157603479801, 0.08901501908297373, 0.6534154490851757, 0.0007772763765484529, 0.1489067370196236, 0.3647766527140929, 0.1077136552683109, 0.0527479558818025, 0.7623382929365795, 0.09219421919803619, 0.05306257599411537, 0.0009595033942378324, 0.01813519326083406, 0.0004019417652746559, 0.4424281751031302, 0.7547642112312916, 0.4713104680135458, 0.006418764538505052, 0.1200692140984003, 0.000134529582172131, 0.9100069366972939, 0.0004355474440655466, 0.8879760162754001, 0.3137233405902848, 0.0225571724414577, 0.2529682316422089, 0.0228948892170381, 0.007001999689320019, 0.001246721801592243, 0.1024569910433331, 0.001892980244998611, 0.112944998445729, 0.00315087752858573, 0.9214829120921572, 0.2640407241864675, 0.5708155013456935, 0.2172941984956976, 0.9558558627734214, 0.960603955986077, 0.02892283973146204] 
  ],
 "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. Version 3.1 adds HMM auto-correlation option for SRV, and binds SRV distributions for multiple branch sets\n",
   "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
   "version":"3.1"
  },
 "background":0,
 "branch attributes":{
   "0":{
     "Baboon":{
       "MG94xREV with separate rates for branch sets":0.001772434847524003,
       "Nucleotide GTR":0.001680040630127455,
       "constrained":0.001513413708231178,
       "original name":"Baboon",
       "unconstrained":0.00161713005248515
      },
     "Cat":{
       "MG94xREV with separate rates for branch sets":0.2735065373507703,
       "Nucleotide GTR":0.2660909938917123,
       "constrained":0.3466844629529476,
       "original name":"Cat",
       "unconstrained":0.3607268493024173
      },
     "Chimp":{
       "MG94xREV with separate rates for branch sets":0.001828401123834132,
       "Nucleotide GTR":0.001818373670119325,
       "constrained":0.001854421055569225,
       "original name":"Chimp",
       "unconstrained":0.001853794709397617
      },
     "Cow":{
       "MG94xREV with separate rates for branch sets":0.2477981038577003,
       "Nucleotide GTR":0.2481025999892287,
       "constrained":0.3115800338446564,
       "original name":"Cow",
       "unconstrained":0.3266266518611717
      },
     "Horse":{
       "MG94xREV with separate rates for branch sets":0.21116782461044,
       "Nucleotide GTR":0.2090310577070883,
       "constrained":0.2473423214593362,
       "original name":"Horse",
       "unconstrained":0.2568895651944081
      },
     "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":0.1200804161847832,
       "Nucleotide GTR":0.1180171198334285,
       "constrained":0.1381882260320684,
       "original name":"Mouse",
       "unconstrained":0.1482500840848965
      },
     "Node1":{
       "MG94xREV with separate rates for branch sets":0.2841417945012228,
       "Nucleotide GTR":0.2767237570684924,
       "constrained":0.3893703941610758,
       "unconstrained":0.4535373691584812
      },
     "Node12":{
       "MG94xREV with separate rates for branch sets":0.01789005959388253,
       "Nucleotide GTR":0.01784803874223016,
       "constrained":0.01603697675468384,
       "unconstrained":0.01716581823757766
      },
     "Node2":{
       "MG94xREV with separate rates for branch sets":0.06425321743363792,
       "Nucleotide GTR":0.06613162123865737,
       "constrained":0.06766882319669908,
       "unconstrained":0.06748821329187271
      },
     "Node3":{
       "MG94xREV with separate rates for branch sets":0.1017634409613201,
       "Nucleotide GTR":0.09886326330774685,
       "constrained":0.128627313187861,
       "unconstrained":0.1385358286963005
      },
     "Node8":{
       "MG94xREV with separate rates for branch sets":0.1095532710088725,
       "Nucleotide GTR":0.106239268140425,
       "constrained":0.1326559254556453,
       "unconstrained":0.1430782720540034
      },
     "Node9":{
       "MG94xREV with separate rates for branch sets":0.02590764371262369,
       "Nucleotide GTR":0.02566573875750134,
       "constrained":0.02991066003065707,
       "unconstrained":0.02952913741456189
      },
     "Pig":{
       "MG94xREV with separate rates for branch sets":0.1925158663261413,
       "Nucleotide GTR":0.1871893456388788,
       "constrained":0.2351007649069627,
       "original name":"Pig",
       "unconstrained":0.248176820169511
      },
     "Rat":{
       "MG94xREV with separate rates for branch sets":0.06699144002108472,
       "Nucleotide GTR":0.06661283005976348,
       "constrained":0.06832918896283274,
       "original name":"Rat",
       "unconstrained":0.07114161288708017
      },
     "RhMonkey":{
       "MG94xREV with separate rates for branch sets":0.003716234330029482,
       "Nucleotide GTR":0.003775170135617877,
       "constrained":0.004078975866589158,
       "original name":"RhMonkey",
       "unconstrained":0.003977618821878279
      }
    },
   "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":6918.865252134614,
     "Log Likelihood":-3419.580167050914,
     "Rate Distributions":{
       "Synonymous site-to-site rates":{
         "0":{
           "proportion":0.3286044813984554,
           "rate":0.3114745230555425
          },
         "1":{
           "proportion":0.5759073485616787,
           "rate":1.038727366194607
          },
         "2":{
           "proportion":0.09548817003986594,
           "rate":3.135858111155513
          }
        },
       "Test":{
         "0":{
           "omega":0,
           "proportion":0.1610337459523823
          },
         "1":{
           "omega":0.9239856235614761,
           "proportion":0
          },
         "2":{
           "omega":1,
           "proportion":0.8389662540476177
          }
        }
      },
     "display order":3,
     "estimated parameters":39
    },
   "MG94xREV with separate rates for branch sets":{
     "AIC-c":6997.104847699299,
     "Equilibrium frequencies":      [
[0.04876086397632926],
      [0.03982224127745371],
      [0.0494959405650269],
      [0.04152830682371345],
      [0.01810345074594235],
      [0.01478480742075003],
      [0.01837636270304883],
      [0.01541821854326533],
      [0.01892910005547028],
      [0.01545910240515689],
      [0.01921445878706794],
      [0.01612140169177368],
      [0.02829747763884322],
      [0.02311011106415996],
      [0.02872406592369408],
      [0.02410019507229243],
      [0.01663805943190806],
      [0.01358804506433061],
      [0.01688888041768248],
      [0.01417018446135155],
      [0.006177213955434187],
      [0.005044834822351987],
      [0.006270336287397383],
      [0.00526096577332031],
      [0.006458939937330408],
      [0.005274916061901906],
      [0.006556309326397028],
      [0.005500904159606446],
      [0.009655594186286731],
      [0.007885574003572761],
      [0.009801153568494354],
      [0.008223407979974132],
      [0.03327785448210915],
      [0.02717750758119989],
      [0.03377952261833742],
      [0.02834184710178207],
      [0.01235507229404208],
      [0.01009019590244688],
      [0.01254132667213156],
      [0.01052248035033209],
      [0.01291855364640413],
      [0.01055038238273567],
      [0.01311330258173711],
      [0.01100238215235291],
      [0.01931219560697892],
      [0.0157719705998612],
      [0.01960332955558842],
      [0.01644767379420349],
      [0.01965132601881859],
      [0.02049322866376102],
      [0.008933621043463411],
      [0.007295949736387736],
      [0.009068296583349953],
      [0.007608523013862737],
      [0.007628698224327205],
      [0.009481877006094248],
      [0.00795552712159237],
      [0.01396413011303752],
      [0.01140428846505027],
      [0.01417464125436193],
      [0.01189287130232129] 
      ],
     "Log Likelihood":-3467.012706765863,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *test*":        [
[0.9959842858928788, 1] 
        ]
      },
     "display order":1,
     "estimated parameters":31
    },
   "Nucleotide GTR":{
     "AIC-c":7112.857310169033,
     "Equilibrium frequencies":      [
[0.3592490842490842],
      [0.181959706959707],
      [0.240018315018315],
      [0.2187728937728937] 
      ],
     "Log Likelihood":-3532.32122446679,
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0.2647746107611847,
       "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032,
       "Substitution rate from nucleotide C to nucleotide T":1.02837595903795,
       "Substitution rate from nucleotide G to nucleotide T":0.304509117524575
      },
     "display order":0,
     "estimated parameters":24
    },
   "Unconstrained model":{
     "AIC-c":6910.776988890891,
     "Log Likelihood":-3414.491829601268,
     "Rate Distributions":{
       "Synonymous site-to-site rates":{
         "0":{
           "proportion":0.2655037162058198,
           "rate":0.2749303122566129
          },
         "1":{
           "proportion":0.6321791898264187,
           "rate":0.9740711294478059
          },
         "2":{
           "proportion":0.1023170939677615,
           "rate":3.041695877803997
          }
        },
       "Test":{
         "0":{
           "omega":0,
           "proportion":0.386646389823596
          },
         "1":{
           "omega":0.9964438830494696,
           "proportion":0
          },
         "2":{
           "omega":1.876622752045829,
           "proportion":0.613353610176404
          }
        }
      },
     "display order":2,
     "estimated parameters":40
    }
  },
 "input":{
   "file name":"/tmp/tmpfqvtss8b/job_working_directory/000/3/working/./input.fasta",
   "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":10.17667489929045,
   "p-value":0.003084133210483175
  },
 "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":70
    },
   "Overall":{
     "order":0,
     "timer":451
    },
   "Preliminary model fitting":{
     "order":1,
     "timer":10
    },
   "Unconstrained BUSTED model fitting":{
     "order":2,
     "timer":370
    }
  }
}