view test-data/bgm-out1.json @ 1:b678fe748dc5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"

{
 "MLE":{
   "content":    [
[3, 4, 0.01806536842133838, 0.0196151052739404, 0.03768047369527878, 2, 4, 1],
    [3, 5, 0.0136689326165866, 0.08411879896894461, 0.09778773158553121, 2, 2, 1],
    [3, 6, 0.01626880980001384, 0.05621779910581199, 0.07248660890582583, 2, 2, 1],
    [3, 7, 0.01296085994820069, 0.02206081801264715, 0.03502167796084783, 2, 1, 0],
    [3, 9, 0.01069476203525126, 0.01376808584576788, 0.02446284788101914, 2, 3, 0],
    [3, 10, 0.05465425513197631, 0.1433115560788012, 0.1979658112107776, 2, 1, 1],
    [3, 11, 0.02893963856420952, 0.01605584764833427, 0.04499548621254379, 2, 1, 0],
    [3, 12, 0.01072516405613842, 0.0249434485528662, 0.03566861260900463, 2, 1, 0],
    [3, 14, 0.02105948857071199, 0.05408645518169206, 0.07514594375240405, 2, 2, 1],
    [3, 15, 0.0123000231875007, 0.02432900062064017, 0.03662902380814088, 2, 3, 1],
    [3, 16, 0.005326227185235535, 0.02715178476956077, 0.0324780119547963, 2, 4, 1],
    [3, 17, 0.03377277022598092, 0.04443847194728315, 0.07821124217326408, 2, 2, 1],
    [3, 18, 0.01498654024671119, 0.01399705284721538, 0.02898359309392656, 2, 2, 0],
    [3, 20, 0.03160117895292701, 0.03379356385898681, 0.06539474281191382, 2, 3, 1],
    [3, 21, 0.005825814343840907, 0.01762290041418722, 0.02344871475802813, 2, 5, 1],
    [3, 22, 0.004808842565391303, 0.01857986311191453, 0.02338870567730583, 2, 5, 1],
    [3, 23, 0.01560225549428971, 0.01369335589628938, 0.02929561139057909, 2, 3, 0],
    [3, 24, 0.02796792379060828, 0.0120172661798151, 0.03998518997042338, 2, 2, 0],
    [3, 25, 0.004879890854338218, 0.05174659736268138, 0.05662648821701959, 2, 3, 1],
    [3, 26, 0.008542556433088364, 0.02342067235707167, 0.03196322879016003, 2, 1, 0],
    [3, 28, 0.02842598870361674, 0.04882702442678508, 0.07725301313040182, 2, 2, 1],
    [3, 29, 0.02983611705240465, 0.04834281650968934, 0.07817893356209399, 2, 2, 1],
    [3, 30, 0.02136530753356511, 0.056551049600131, 0.0779163571336961, 2, 2, 1],
    [4, 5, 0.04128639081201998, 0.1643521228119713, 0.2056385136239913, 4, 2, 2],
    [4, 6, 0.002891680521324363, 0.02014100082658794, 0.0230326813479123, 4, 2, 1],
    [4, 7, 0.01937071123900217, 0.03955420345740617, 0.05892491469640834, 4, 1, 1],
    [4, 9, 0.005876622911646858, 0.01316366694762399, 0.01904028985927084, 4, 3, 1],
    [4, 10, 0.02063883956421052, 0.03235708509290364, 0.05299592465711416, 4, 1, 1],
    [4, 11, 0.05646705485150577, 0.03046422064113512, 0.08693127549264089, 4, 1, 1],
    [4, 12, 0.018550325874111, 0.04456585108483763, 0.06311617695894862, 4, 1, 1],
    [4, 14, 0.002644483178150749, 0.02400887432195999, 0.02665335750011074, 4, 2, 1],
    [4, 15, 0.01378625971212575, 0.03709407143284885, 0.05088033114497461, 4, 3, 2],
    [4, 16, 0.005366210549264398, 0.0254419855729714, 0.03080819612223579, 4, 4, 2],
    [4, 17, 0.08506807888824773, 0.08873474434715359, 0.1738028232354013, 4, 2, 2],
    [4, 18, 0.01666065271395927, 0.01550783907099662, 0.03216849178495589, 4, 2, 1],
    [4, 20, 0.0602710511807769, 0.03562465630098035, 0.09589570748175724, 4, 3, 2],
    [4, 21, 0.03064565490801606, 0.06355132795273535, 0.09419698286075141, 4, 5, 3],
    [4, 22, 0.02451199601165472, 0.07489768093572295, 0.09940967694737768, 4, 5, 3],
    [4, 23, 0.03630394203907011, 0.03058821944652209, 0.06689216148559221, 4, 3, 2],
    [4, 24, 0.02164778178638001, 0.008961778863845419, 0.03060956065022543, 4, 2, 0],
    [4, 25, 0.01168690527839325, 0.07747501344981376, 0.08916191872820702, 4, 3, 2],
    [4, 26, 0.01588288283660194, 0.04096522221306678, 0.05684810504966872, 4, 1, 1],
    [4, 28, 0.01128665086452497, 0.01582662360389917, 0.02711327446842414, 4, 2, 1],
    [4, 29, 0.01028593387764938, 0.01547886135935664, 0.02576479523700602, 4, 2, 1],
    [4, 30, 0.004517730197507495, 0.02179721676324585, 0.02631494696075334, 4, 2, 1],
    [5, 6, 0.01349845941886215, 0.0271001713778612, 0.04059863079672335, 2, 2, 1],
    [5, 7, 0.08386293017699854, 0.05547962590044048, 0.139342556077439, 2, 1, 1],
    [5, 9, 0.01976650604639912, 0.01082947702714442, 0.03059598307354354, 2, 3, 1],
    [5, 10, 0.08663121746727073, 0.05454639965761584, 0.1411776171248866, 2, 1, 1],
    [5, 11, 0.03770763685855846, 0.006284585998205416, 0.04399222285676388, 2, 1, 0],
    [5, 12, 0.1076906900926125, 0.0473111213301104, 0.1550018114227228, 2, 1, 1],
    [5, 14, 0.01972942054521223, 0.0320506800558711, 0.05178010060108334, 2, 2, 1],
    [5, 15, 0.0115296223772864, 0.009425622068293078, 0.02095524444557947, 2, 3, 1],
    [5, 16, 0.05795468769109502, 0.07437721131546923, 0.1323318990065643, 2, 4, 2],
    [5, 17, 0.04893957970901563, 0.01779579930892645, 0.06673537901794209, 2, 2, 1],
    [5, 18, 0.06914575237510151, 0.01277854849843139, 0.08192430087353289, 2, 2, 1],
    [5, 20, 0.04606204168737617, 0.008407721695554574, 0.05446976338293075, 2, 3, 1],
    [5, 21, 0.06137939961987368, 0.03626744029311923, 0.09764683991299292, 2, 5, 2],
    [5, 22, 0.04000126166279955, 0.03754521666039747, 0.07754647832319703, 2, 5, 2],
    [5, 23, 0.03357555220343731, 0.01381372812520867, 0.04738928032864598, 2, 3, 1],
    [5, 24, 0.03380670133572664, 0.003731548300121901, 0.03753824963584854, 2, 2, 0],
    [5, 25, 0.09004803803938788, 0.2417884826530335, 0.3318365206924214, 2, 3, 2],
    [5, 26, 0.08754942747826591, 0.05315050503462983, 0.1406999325128958, 2, 1, 1],
    [5, 28, 0.04567502066103889, 0.01808010305875397, 0.06375512371979286, 2, 2, 1],
    [5, 29, 0.03260950473238529, 0.02317187888808829, 0.05578138362047358, 2, 2, 1],
    [5, 30, 0.02112358475746083, 0.02897865767093947, 0.05010224242840029, 2, 2, 1],
    [6, 7, 0.01668462680139263, 0.009946683404740683, 0.02663131020613331, 2, 1, 0],
    [6, 9, 0.01988584439856818, 0.009045415077913333, 0.02893125947648151, 2, 3, 1],
    [6, 10, 0.07997756465918539, 0.02777823877936857, 0.107755803438554, 2, 1, 1],
    [6, 11, 0.0427529051299776, 0.004277233013937032, 0.04703013814391463, 2, 1, 0],
    [6, 12, 0.01457894161504904, 0.0107389078090505, 0.02531784942409954, 2, 1, 0],
    [6, 14, 0.2325712692000255, 0.2014841220660465, 0.4340553912660721, 2, 2, 2],
    [6, 15, 0.1692106649881499, 0.05297107692530162, 0.2221817419134515, 2, 3, 2],
    [6, 16, 0.05738158701493928, 0.04589333277643135, 0.1032749197913706, 2, 4, 2],
    [6, 17, 0.04815193631537981, 0.009529021235036772, 0.05768095755041659, 2, 2, 1],
    [6, 18, 0.01912767387535096, 0.002044170024231443, 0.0211718438995824, 2, 2, 0],
    [6, 20, 0.02061887763751207, 0.004752091964805672, 0.02537096960231774, 2, 3, 0],
    [6, 21, 0.04247087838195826, 0.02528613276636166, 0.06775701114831992, 2, 5, 2],
    [6, 22, 0.04642062375115955, 0.02142488295951156, 0.06784550671067111, 2, 5, 2],
    [6, 23, 0.01554561721459279, 0.006425146203498221, 0.02197076341809101, 2, 3, 0],
    [6, 24, 0.03314786253017613, 0.001917115026076292, 0.03506497755625242, 2, 2, 0],
    [6, 25, 0.0940662182949361, 0.1384869187847857, 0.2325531370797218, 2, 3, 2],
    [6, 26, 0.01345296901600206, 0.004879799683521298, 0.01833276869952336, 2, 1, 0],
    [6, 28, 0.03796224039722292, 0.007515605266225617, 0.04547784566344854, 2, 2, 1],
    [6, 29, 0.05130583555953379, 0.01021357548333445, 0.06151941104286825, 2, 2, 1],
    [6, 30, 0.2318428453473779, 0.2372832334677343, 0.4691260788151123, 2, 2, 2],
    [7, 9, 0.04510729938504034, 0.033455377610294, 0.07856267699533434, 1, 3, 1],
    [7, 10, 0.01448672927711553, 0.01471180827475936, 0.0291985375518749, 1, 1, 0],
    [7, 11, 0.04558043072600854, 0.01092269815769229, 0.05650312888370083, 1, 1, 0],
    [7, 12, 0.180236004387841, 0.1473331361936553, 0.3275691405814962, 1, 1, 1],
    [7, 14, 0.004060491038913412, 0.009736071123258729, 0.01379656216217214, 1, 2, 0],
    [7, 15, 0.007246951454732821, 0.008020333839217355, 0.01526728529395018, 1, 3, 0],
    [7, 16, 0.02266593379543114, 0.02916472528901524, 0.05183065908444638, 1, 4, 1],
    [7, 17, 0.01353159955561796, 0.006519983350346921, 0.02005158290596488, 1, 2, 0],
    [7, 18, 0.1260783187676728, 0.05727101709727531, 0.1833493358649481, 1, 2, 1],
    [7, 20, 0.09497180416371181, 0.03920153451995714, 0.134173338683669, 1, 3, 1],
    [7, 21, 0.01391734233658772, 0.01774896716072902, 0.03166630949731674, 1, 5, 1],
    [7, 22, 0.01403403421609152, 0.02021415605799259, 0.03424819027408411, 1, 5, 1],
    [7, 23, 0.07875763940318095, 0.02839812636719212, 0.1071557657703731, 1, 3, 1],
    [7, 24, 0.04219288785522956, 0.006992293554900667, 0.04918518141013023, 1, 2, 0],
    [7, 25, 0.01888383639176133, 0.07660835994985157, 0.09549219634161291, 1, 3, 1],
    [7, 26, 0.1593820711044853, 0.1731736129027814, 0.3325556840072666, 1, 1, 1],
    [7, 28, 0.01379492231999666, 0.008854310031253648, 0.0226492323512503, 1, 2, 0],
    [7, 29, 0.01318267142576915, 0.01115280933551254, 0.02433548076128169, 1, 2, 0],
    [7, 30, 0.005464156565736539, 0.01604643247941549, 0.02151058904515203, 1, 2, 0],
    [9, 10, 0.008743328720289559, 0.008998664007820409, 0.01774199272810997, 3, 1, 0],
    [9, 11, 0.02301313307916227, 0.008353618087185346, 0.03136675116634761, 3, 1, 0],
    [9, 12, 0.03485480851874616, 0.0385220468500885, 0.07337685536883466, 3, 1, 1],
    [9, 14, 0.00925561597787489, 0.02345072843860894, 0.03270634441648383, 3, 2, 1],
    [9, 15, 0.005885707639577632, 0.0093457630141815, 0.01523147065375913, 3, 3, 1],
    [9, 16, 0.1352472349062049, 0.4258754197367833, 0.5611226546429883, 3, 4, 3],
    [9, 17, 0.0114528061541329, 0.009382339097390304, 0.0208351452515232, 3, 2, 0],
    [9, 18, 0.02851553908154206, 0.01525552104269379, 0.04377106012423586, 3, 2, 1],
    [9, 20, 0.01822901326926599, 0.01058740382851504, 0.02881641709778102, 3, 3, 1],
    [9, 21, 0.01637284646045184, 0.01528766975294247, 0.03166051621339431, 3, 5, 2],
    [9, 22, 0.01125203456673749, 0.01471364636147226, 0.02596568092820975, 3, 5, 2],
    [9, 23, 0.01581371454122383, 0.008723591174246868, 0.02453730571547069, 3, 3, 1],
    [9, 24, 0.04988705657909906, 0.01387214589279543, 0.06375920247189448, 3, 2, 1],
    [9, 25, 0.02481744876612966, 0.09561117569876813, 0.1204286244648978, 3, 3, 2],
    [9, 26, 0.02474648571293647, 0.05329817226044276, 0.07804465797337923, 3, 1, 1],
    [9, 28, 0.0133763748141426, 0.01726376204208423, 0.03064013685622684, 3, 2, 1],
    [9, 29, 0.01447958284562607, 0.02105672282873693, 0.03553630567436301, 3, 2, 1],
    [9, 30, 0.004787350233147937, 0.02258996514478861, 0.02737731537793655, 3, 2, 1],
    [10, 11, 0.04076687919145038, 0.01600339189308192, 0.05677027108453229, 1, 1, 0],
    [10, 12, 0.01487003942060377, 0.01285394941082142, 0.02772398883142518, 1, 1, 0],
    [10, 14, 0.0278020913930161, 0.06116723064367017, 0.08896932203668627, 1, 2, 1],
    [10, 15, 0.02590065104611214, 0.04413779140155937, 0.07003844244767152, 1, 3, 1],
    [10, 16, 0.01473871457697519, 0.03900854939746186, 0.05374726397443705, 1, 4, 1],
    [10, 17, 0.07737832850149316, 0.04512778545801077, 0.1225061139595039, 1, 2, 1],
    [10, 18, 0.01848975784724837, 0.00977696218399207, 0.02826672003124044, 1, 2, 0],
    [10, 20, 0.02248228077129723, 0.006391817662418776, 0.028874098433716, 1, 3, 0],
    [10, 21, 0.01548391498233171, 0.01956514936920832, 0.03504906435154003, 1, 5, 1],
    [10, 22, 0.01618209456972476, 0.02198162318745958, 0.03816371775718434, 1, 5, 1],
    [10, 23, 0.01304324890636816, 0.007815357572873324, 0.02085860647924148, 1, 3, 0],
    [10, 24, 0.03420490961110176, 0.008535296159903609, 0.04274020577100537, 1, 2, 0],
    [10, 25, 0.0147192856248153, 0.06581358768988828, 0.08053287331470357, 1, 3, 1],
    [10, 26, 0.01551389889619659, 0.02137375724421267, 0.03688765614040926, 1, 1, 0],
    [10, 28, 0.08242337980044148, 0.06924953639794011, 0.1516729161983816, 1, 2, 1],
    [10, 29, 0.0486391168101336, 0.06529494069867375, 0.1139340575088074, 1, 2, 1],
    [10, 30, 0.03219208960454593, 0.08832014266169741, 0.1205122322662433, 1, 2, 1],
    [11, 12, 0.0083422559528536, 0.04577125284234392, 0.05411350879519752, 1, 1, 0],
    [11, 14, 0.003063442830455156, 0.03058506004416841, 0.03364850287462357, 1, 2, 0],
    [11, 15, 0.008700688461801026, 0.02837240877883479, 0.03707309724063582, 1, 3, 0],
    [11, 16, 0.002513035135905159, 0.033081097723843, 0.03559413285974816, 1, 4, 0],
    [11, 17, 0.01015972517797896, 0.02585886367401776, 0.03601858885199673, 1, 2, 0],
    [11, 18, 0.01760510226017101, 0.02599830916230194, 0.04360341142247295, 1, 2, 0],
    [11, 20, 0.01570796171982357, 0.02432862307641051, 0.04003658479623408, 1, 3, 0],
    [11, 21, 0.005149376434442727, 0.02438894100547246, 0.02953831743991518, 1, 5, 0],
    [11, 22, 0.009744174308072966, 0.02717998704157922, 0.03692416134965219, 1, 5, 0],
    [11, 23, 0.0112816847864048, 0.02443013410042389, 0.0357118188868287, 1, 3, 0],
    [11, 24, 0.02611002944106307, 0.0243078721393825, 0.05041790158044557, 1, 2, 0],
    [11, 25, 0.00220817709319456, 0.04746832197244566, 0.04967649906564022, 1, 3, 0],
    [11, 26, 0.01079476529061294, 0.04998538352365951, 0.06078014881427245, 1, 1, 0],
    [11, 28, 0.007641379119979673, 0.03338702752077345, 0.04102840664075313, 1, 2, 0],
    [11, 29, 0.007824939016498385, 0.03557816199737629, 0.04340310101387468, 1, 2, 0],
    [11, 30, 0.002863447023878826, 0.03959507498879136, 0.04245852201267018, 1, 2, 0],
    [12, 14, 0.003531669272860574, 0.01503022692694298, 0.01856189619980356, 1, 2, 0],
    [12, 15, 0.005687502712301731, 0.009779382902868514, 0.01546688561517024, 1, 3, 0],
    [12, 16, 0.01897951429643458, 0.03338924626281588, 0.05236876055925047, 1, 4, 1],
    [12, 17, 0.01327573410150146, 0.008423500238909153, 0.02169923434041061, 1, 2, 0],
    [12, 18, 0.1492207326112999, 0.04435218220084611, 0.193572914812146, 1, 2, 1],
    [12, 20, 0.08617756897569587, 0.03342886351154893, 0.1196064324872448, 1, 3, 1],
    [12, 21, 0.01285874706488638, 0.01979657138334778, 0.03265531844823416, 1, 5, 1],
    [12, 22, 0.01379762818626092, 0.01723547685811808, 0.03103310504437899, 1, 5, 1],
    [12, 23, 0.06866921830001689, 0.0301984941528498, 0.09886771245286669, 1, 3, 1],
    [12, 24, 0.03515608866627348, 0.008300090752201086, 0.04345617941847457, 1, 2, 0],
    [12, 25, 0.02112831751687818, 0.07223272662848533, 0.09336104414536352, 1, 3, 1],
    [12, 26, 0.1775091239215047, 0.1611450236151337, 0.3386541475366385, 1, 1, 1],
    [12, 28, 0.01239927190285539, 0.010630447602192, 0.02302971950504739, 1, 2, 0],
    [12, 29, 0.01305671059301914, 0.009969589662362952, 0.0230263002553821, 1, 2, 0],
    [12, 30, 0.006106520807643618, 0.01501964804331584, 0.02112616885095946, 1, 2, 0],
    [14, 15, 0.1240062700965975, 0.07055023087280403, 0.1945565009694015, 2, 3, 2],
    [14, 16, 0.04968169518424277, 0.04322317133962539, 0.09290486652386816, 2, 4, 2],
    [14, 17, 0.03301523267075585, 0.006938602753590835, 0.03995383542434668, 2, 2, 1],
    [14, 18, 0.02006635669718209, 0.0042781821914317, 0.02434453888861379, 2, 2, 0],
    [14, 20, 0.02233301521846701, 0.003089474062639977, 0.02542248928110699, 2, 3, 0],
    [14, 21, 0.03948359355880873, 0.03409086082661509, 0.07357445438542382, 2, 5, 2],
    [14, 22, 0.0268688773450427, 0.0214401774126719, 0.0483090547577146, 2, 5, 2],
    [14, 23, 0.01484527139830796, 0.004437309946058014, 0.01928258134436597, 2, 3, 0],
    [14, 24, 0.03462721449579641, 0.003757871643734362, 0.03838508613953077, 2, 2, 0],
    [14, 25, 0.06357218444057811, 0.1549937645200927, 0.2185659489606708, 2, 3, 2],
    [14, 26, 0.01465463614671243, 0.003872792297083958, 0.01852742844379638, 2, 1, 0],
    [14, 28, 0.03514614576841267, 0.01055993418218698, 0.04570607995059965, 2, 2, 1],
    [14, 29, 0.03706388753758103, 0.00812869954206062, 0.04519258707964165, 2, 2, 1],
    [14, 30, 0.2282750950032041, 0.2310589775978077, 0.4593340726010118, 2, 2, 2],
    [15, 16, 0.01428121180297797, 0.03049560777140135, 0.04477681957437932, 3, 4, 2],
    [15, 17, 0.2365900473291059, 0.06430920229086168, 0.3008992496199676, 3, 2, 2],
    [15, 18, 0.01866802394433401, 0.003914994869448416, 0.02258301881378243, 3, 2, 0],
    [15, 20, 0.02356819283235103, 0.005400571337284119, 0.02896876416963515, 3, 3, 1],
    [15, 21, 0.1063655984295545, 0.1098520926697359, 0.2162176910992904, 3, 5, 3],
    [15, 22, 0.113078754604692, 0.1193807004556669, 0.2324594550603589, 3, 5, 3],
    [15, 23, 0.01760198994331581, 0.004394350408904264, 0.02199634035222007, 3, 3, 1],
    [15, 24, 0.0255055798649768, 0.003455505302173749, 0.02896108516715055, 3, 2, 0],
    [15, 25, 0.02286215331427334, 0.05572789891617332, 0.07859005223044666, 3, 3, 2],
    [15, 26, 0.01144159443320607, 0.005868313383528745, 0.01730990781673482, 3, 1, 0],
    [15, 28, 0.01363916550740871, 0.01152910521301816, 0.02516827072042686, 3, 2, 1],
    [15, 29, 0.01851254280568752, 0.01005463911380465, 0.02856718191949216, 3, 2, 1],
    [15, 30, 0.07122084719427205, 0.1468009520008997, 0.2180217991951718, 3, 2, 2],
    [16, 17, 0.01782636504763381, 0.004049733645987459, 0.02187609869362126, 4, 2, 1],
    [16, 18, 0.02901428767197188, 0.007979068596454607, 0.03699335626842649, 4, 2, 1],
    [16, 20, 0.02145658661219722, 0.004828023565954753, 0.02628461017815198, 4, 3, 1],
    [16, 21, 0.04160074147630265, 0.0207606784884952, 0.06236141996479785, 4, 5, 3],
    [16, 22, 0.05146197934676123, 0.01823400830047511, 0.06969598764723633, 4, 5, 3],
    [16, 23, 0.01822949401965692, 0.003315249491921823, 0.02154474351157875, 4, 3, 1],
    [16, 24, 0.03676885352758808, 0.006253436543370671, 0.04302229007095875, 4, 2, 1],
    [16, 25, 0.1841429087738894, 0.3152593422346555, 0.4994022510085449, 4, 3, 3],
    [16, 26, 0.03417832955442882, 0.01682864955963237, 0.05100697911406119, 4, 1, 1],
    [16, 28, 0.09860322016656659, 0.04068814080185486, 0.1392913609684215, 4, 2, 2],
    [16, 29, 0.1080970519952679, 0.03688377612775603, 0.144980828123024, 4, 2, 2],
    [16, 30, 0.0377960989989632, 0.06418358230375337, 0.1019796813027166, 4, 2, 2],
    [17, 18, 0.01185456228440142, 0.007796983061071273, 0.01965154534547269, 2, 2, 0],
    [17, 20, 0.0332281399389085, 0.01516984390639092, 0.04839798384529942, 2, 3, 1],
    [17, 21, 0.03131317673510807, 0.04980166629871462, 0.08111484303382269, 2, 5, 2],
    [17, 22, 0.02658918454287775, 0.05018726477890903, 0.07677644932178679, 2, 5, 2],
    [17, 23, 0.02475247746828598, 0.0169563833600419, 0.04170886082832788, 2, 3, 1],
    [17, 24, 0.02250824430772414, 0.006885755628265392, 0.02939399993598953, 2, 2, 0],
    [17, 25, 0.008406025942038792, 0.03106161612057492, 0.03946764206261372, 2, 3, 1],
    [17, 26, 0.009282829245117721, 0.01432266485153354, 0.02360549409665125, 2, 1, 0],
    [17, 28, 0.02505746434873073, 0.02439269819223868, 0.04945016254096941, 2, 2, 1],
    [17, 29, 0.02334545268294474, 0.02603360928442499, 0.04937906196736973, 2, 2, 1],
    [17, 30, 0.006120114170392863, 0.04613425130634214, 0.052254365476735, 2, 2, 1],
    [18, 20, 0.02835867055729394, 0.03051095907045615, 0.05886962962775009, 2, 3, 1],
    [18, 21, 0.006524067143595717, 0.02097381073320005, 0.02749787787679577, 2, 5, 1],
    [18, 22, 0.005951114890757478, 0.01734555223255374, 0.02329666712331122, 2, 5, 1],
    [18, 23, 0.02679758037211821, 0.02171809821499259, 0.0485156785871108, 2, 3, 1],
    [18, 24, 0.02794861768861829, 0.01091010179620578, 0.03885871948482407, 2, 2, 0],
    [18, 25, 0.00547466390308578, 0.05096953940013922, 0.056444203303225, 2, 3, 1],
    [18, 26, 0.04713529782381884, 0.147517174759375, 0.1946524725831938, 2, 1, 1],
    [18, 28, 0.005834608457505859, 0.0152237752272461, 0.02105838368475195, 2, 2, 0],
    [18, 29, 0.009809673821294161, 0.01961999091486498, 0.02942966473615914, 2, 2, 0],
    [18, 30, 0.004106924911106094, 0.0212640024303487, 0.02537092734145479, 2, 2, 0],
    [20, 21, 0.0106282403425438, 0.04039821513711003, 0.05102645547965383, 3, 5, 2],
    [20, 22, 0.01018346538718277, 0.03712847397201344, 0.0473119393591962, 3, 5, 2],
    [20, 23, 0.08066982082609707, 0.09697970751966636, 0.1776495283457634, 3, 3, 2],
    [20, 24, 0.0235382382132855, 0.01604967777748543, 0.03958791599077093, 3, 2, 0],
    [20, 25, 0.003423699228229319, 0.03729116441894532, 0.04071486364717464, 3, 3, 1],
    [20, 26, 0.03010903973132922, 0.0792493655437253, 0.1093584052750545, 3, 1, 1],
    [20, 28, 0.006896520869508807, 0.01763535757626972, 0.02453187844577853, 3, 2, 0],
    [20, 29, 0.008452797226508749, 0.01635647793775643, 0.02480927516426518, 3, 2, 0],
    [20, 30, 0.003095558108305428, 0.02500421480139507, 0.0280997729097005, 3, 2, 0],
    [21, 22, 0.1252684968513963, 0.136515693167626, 0.2617841900190223, 5, 5, 4],
    [21, 23, 0.03150028194750475, 0.01038169657309909, 0.04188197852060385, 5, 3, 2],
    [21, 24, 0.0291189462349777, 0.004949542712431419, 0.03406848894740912, 5, 2, 0],
    [21, 25, 0.05817486040851345, 0.2337789498314103, 0.2919538102399237, 5, 3, 3],
    [21, 26, 0.02161672916870432, 0.01542046740137113, 0.03703719657007545, 5, 1, 1],
    [21, 28, 0.008853112135224245, 0.01473257967171467, 0.02358569180693892, 5, 2, 1],
    [21, 29, 0.01104149126852355, 0.0112121954071869, 0.02225368667571045, 5, 2, 1],
    [21, 30, 0.01981188214469076, 0.04607061916870642, 0.06588250131339718, 5, 2, 2],
    [22, 23, 0.2417023075963993, 0.09748281763954433, 0.3391851252359436, 5, 3, 3],
    [22, 24, 0.02866820036560731, 0.004389002955129634, 0.03305720332073694, 5, 2, 1],
    [22, 25, 0.05951378230290671, 0.2182001187994253, 0.277713901102332, 5, 3, 3],
    [22, 26, 0.0216180875663217, 0.01912704074549006, 0.04074512831181176, 5, 1, 1],
    [22, 28, 0.01017154387527456, 0.006751614251023627, 0.01692315812629819, 5, 2, 1],
    [22, 29, 0.008484165669395357, 0.006352798226140098, 0.01483696389553545, 5, 2, 1],
    [22, 30, 0.01671073245892866, 0.04349804879476411, 0.06020878125369277, 5, 2, 2],
    [23, 24, 0.04562441011343223, 0.02002989348257047, 0.0656543035960027, 3, 2, 1],
    [23, 25, 0.002681149687355626, 0.02379196502622149, 0.02647311471357712, 3, 3, 1],
    [23, 26, 0.02520734946693424, 0.08017222321450257, 0.1053795726814368, 3, 1, 1],
    [23, 28, 0.006108324165705776, 0.01315945866988892, 0.0192677828355947, 3, 2, 0],
    [23, 29, 0.007832385982193907, 0.01244156292841715, 0.02027394891061106, 3, 2, 0],
    [23, 30, 0.002148132526385406, 0.0162182445937851, 0.0183663771201705, 3, 2, 0],
    [24, 25, 0.003280169877064053, 0.04232444793320719, 0.04560461781027124, 2, 3, 0],
    [24, 26, 0.005616845573718578, 0.03457432648711956, 0.04019117206083814, 2, 1, 0],
    [24, 28, 0.01662564599904145, 0.08682615622766726, 0.1034518022267087, 2, 2, 1],
    [24, 29, 0.02380609019454122, 0.08066548140193953, 0.1044715715964808, 2, 2, 1],
    [24, 30, 0.001779848103066491, 0.03558210318886525, 0.03736195129193174, 2, 2, 0],
    [25, 26, 0.06593316758122636, 0.02166592663716863, 0.08759909421839499, 3, 1, 1],
    [25, 28, 0.02889704020936961, 0.005342768040509653, 0.03423980824987927, 3, 2, 1],
    [25, 29, 0.02814406496232846, 0.01687874749838335, 0.04502281246071182, 3, 2, 1],
    [25, 30, 0.1123773177282409, 0.107330048901509, 0.2197073666297499, 3, 2, 2],
    [26, 28, 0.01202310187965289, 0.0100752849569055, 0.0220983868365584, 1, 2, 0],
    [26, 29, 0.01098659894875614, 0.0106778458846393, 0.02166444483339544, 1, 2, 0],
    [26, 30, 0.008888531742284057, 0.0220072024775357, 0.03089573421981976, 1, 2, 0],
    [28, 29, 0.3253931306175987, 0.3786081317863912, 0.70400126240399, 2, 2, 2],
    [28, 30, 0.007946759742122602, 0.03360599467213372, 0.04155275441425633, 2, 2, 1],
    [29, 30, 0.01669873349292508, 0.03504162520377113, 0.05174035869669621, 2, 2, 1] 
    ],
   "headers":    [
["Site 1", "Index of site 1"],
    ["Site 2", "Index of site 2"],
    ["P [Site 1 –> Site 2]", "Probability that site 2 is conditionally dependent on site 1"],
    ["P [Site 2 –> Site 1]", "Probability that site 1 is conditionally dependent on site 2"],
    ["P [Site 1 <–> Site 2]", "Probability that sites 1 and 2 are not conditionally independent"],
    ["Site 1 subs", "Substitution counts inferred for Site 1"],
    ["Site 2 subs", "Substitution counts inferred for Site 2"],
    ["Shared subs", "Substitutions shared by both sites"] 
    ]
  },
 "analysis":{
   "authors":"Art FY Poon, Fraser I Lewis, Simon DW Frost and Sergei L Kosakovsky Pond",
   "citation":"Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models (2008). _Bioinformatics_ 24(17): 1949-1950",
   "contact":"[e-mail]",
   "info":"BGM (Bayesian Graphical Model) uses a maximum likelihood ancestral state reconstruction to\nmap substitution (non-synonymous only for coding data) events to branches in the\nphylogeny and then analyzes the joint distribution of the\nsubstitution map using a Bayesian graphical model (network).\nNext, a Markov chain Monte Carlo analysis is used to generate\na random sample of network structures from the posterior\ndistribution given the data.  Each node in the network\nrepresents a codon site in the alignment, and links (edges)\nbetween nodes indicate high posterior support for correlated\nsubstitutions at the two sites over time, which implies coevolution.",
   "requirements":"in-frame codon alignment and a phylogenetic tree",
   "version":"1.1"
  },
 "branch attributes":{
   "0":{
     "Baboon":{
       "models.DNA.GTR.ModelDescription":0
      },
     "Cat":{
       "models.DNA.GTR.ModelDescription":0.7933191636859576
      },
     "Chimp":{
       "models.DNA.GTR.ModelDescription":0
      },
     "Cow":{
       "models.DNA.GTR.ModelDescription":0.8094119333244753
      },
     "Horse":{
       "models.DNA.GTR.ModelDescription":0.2769077630163064
      },
     "Human":{
       "models.DNA.GTR.ModelDescription":0
      },
     "Mouse":{
       "models.DNA.GTR.ModelDescription":0.1094921058577506
      },
     "Node1":{
       "models.DNA.GTR.ModelDescription":0.4820782253393885
      },
     "Node12":{
       "models.DNA.GTR.ModelDescription":0
      },
     "Node2":{
       "models.DNA.GTR.ModelDescription":0.08259105925424247
      },
     "Node3":{
       "models.DNA.GTR.ModelDescription":0.2526911684326281
      },
     "Node8":{
       "models.DNA.GTR.ModelDescription":0.06531857233184223
      },
     "Node9":{
       "models.DNA.GTR.ModelDescription":0.03361817454867485
      },
     "Pig":{
       "models.DNA.GTR.ModelDescription":0
      },
     "Rat":{
       "models.DNA.GTR.ModelDescription":0.0888784436278628
      },
     "RhMonkey":{
       "models.DNA.GTR.ModelDescription":0
      }
    },
   "attributes":{
     "models.DNA.GTR.ModelDescription":{
       "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] 
      ],
     "name":"bgm.filter.default"
    }
  },
 "fits":{
   "models.DNA.GTR.ModelDescription":{
     "AIC-c":472.7691802214979,
     "Log Likelihood":-210.2027719289308,
     "Rate Distributions":null,
     "display order":0,
     "estimated parameters":24
    }
  },
 "input":{
   "datatype":"nucleotide",
   "file name":"/tmp/tmpSz4m4X/job_working_directory/000/3/working/bgm_input.fa",
   "number of sequences":10,
   "number of sites":30,
   "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)"
    }
  },
 "settings":{
   "burn-in":10000,
   "data-type":"nucleotide",
   "max-parents":1,
   "min-subs":1,
   "samples":100,
   "steps":100000,
   "threshold":0.5
  },
 "tested":0,
 "timers":{
   "Baseline fit":{
     "order":1,
     "timer":0
    },
   "Network inference":{
     "order":2,
     "timer":1
    },
   "Overall":{
     "order":0,
     "timer":1
    }
  }
}