Mercurial > repos > iuc > hyphy_fel

diff test-data/gard-out1.json @ 1:6c3ece5fb602 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
author iuc
date Wed, 21 Aug 2019 12:27:42 -0400
parents
children 8276bb2adea5
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gard-out1.json	Wed Aug 21 12:27:42 2019 -0400
@@ -0,0 +1,318 @@
+{
+ "analysis":{
+   "authors":"Sergei L Kosakovsky Pond",
+   "citation":"**Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm**, _Mol Biol Evol 23(10), 1891–1901",
+   "contact":"spond@temple.edu",
+   "info":"GARD : Genetic Algorithms for Recombination Detection. Implements a heuristic\n    approach to screening alignments of sequences for recombination, by using the CHC genetic algorithm to search for phylogenetic\n    incongruence among different partitions of the data. The number of partitions is determined using a step-up procedure, while the\n    placement of breakpoints is searched for with the GA. The best fitting model (based on c-AIC) is returned; and additional post-hoc\n    tests run to distinguish topological incongruence from rate-variation.",
+   "requirements":"A sequence alignment.",
+   "version":"0.1"
+  },
+ "baselineScore":8884.998566352424,
+ "breakpointData":{
+   "0":{
+     "bps":      [
+[1, 461] 
+      ],
+     "tree":"(((((((TREESPARROW_HENAN_1_2004:0.01973996359641645,TREESPARROW_HENAN_2_2004:0)Node6:0.006601594605919903,CHICKEN_HEBEI_326_2005:0.02877904543700591)Node5:0.002960697265622527,SWINE_ANHUI_2004:0.01220336915594569)Node4:0.004301817483024902,((DUCK_GUANGZHOU_20_2005:0.006496379151101181,(GOOSE_SHANTOU_2216_2005:0.008666763019733412,PEREGRINEFALCON_HK_D0028_2004:0.006494907750172948)Node14:0)Node12:0.006529386248252737,CK_HK_WF157_2003:0.008749819170042668)Node11:0.006517868346508392)Node3:0.004369843971142481,((TREESPARROW_HENAN_3_2004:0.004310725480928182,((CHICKEN_HONGKONG_915_97:0,(HONGKONG_97_98:0.007234718327388172,HONGKONG_538_97:0)Node24:0)Node22:0,(GOOSE_HONGKONG_W355_97:0,DUCK_HONGKONG_Y283_97:0)Node27:0.002160209380619512)Node21:0.02651640051975179)Node19:0.002209468499615626,TREESPARROW_HENAN_4_2004:0.008707376458939551)Node18:0)Node2:0.01527162191938894,MALLARD_VIETNAM_16_2003:0.00216300836609909)Node1:0,HUMAN_VIETNAM_CL105_2005:0.01089634139979296,(((DUCK_VIETNAM_376_2005:0.002165747961920766,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.01092964139649115)Node35:0.002165571630784742,VIETNAM_3062_2004:0)Node34:0.002160659783816526,DUCK_VIETNAM_272_2005:0.006501625005083654)Node33:0)"
+    },
+   "1":{
+     "bps":      [
+[462, 650] 
+      ],
+     "tree":"((((((TREESPARROW_HENAN_1_2004:0,TREESPARROW_HENAN_3_2004:0.01064277225673711)Node5:0.00531987705161906,TREESPARROW_HENAN_2_2004:0)Node4:0.005231591103466107,CHICKEN_HEBEI_326_2005:0.05043188754547531)Node3:0.005435427857192481,CK_HK_WF157_2003:0)Node2:0.005367407450692448,((TREESPARROW_HENAN_4_2004:0.005403333058615208,(((CHICKEN_HONGKONG_915_97:0,(GOOSE_HONGKONG_W355_97:0,DUCK_HONGKONG_Y283_97:0)Node18:0.005303893633648769)Node16:0,HONGKONG_97_98:0)Node15:0,HONGKONG_538_97:0)Node14:0.0160450339521957)Node12:0.01065583332597595,((DUCK_GUANGZHOU_20_2005:0.02156617952480121,GOOSE_SHANTOU_2216_2005:0.005315754078746889)Node24:0,PEREGRINEFALCON_HK_D0028_2004:0.005310132566451705)Node23:0)Node11:0.005324661683629481)Node1:0.01075596871747344,(SWINE_ANHUI_2004:0.01612941661930485,DUCK_VIETNAM_272_2005:0.005332918418299072)Node28:0.005343017103483476,((HUMAN_VIETNAM_CL105_2005:0.01615610619083483,DUCK_VIETNAM_376_2005:0.01622595235090508)Node32:0.005403715853761346,(VIETNAM_3062_2004:0,(MALLARD_VIETNAM_16_2003:0.01066500623689393,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0)Node37:0.005316372444723995)Node35:0)Node31:0)"
+    },
+   "2":{
+     "bps":      [
+[651, 1166] 
+      ],
+     "tree":"(((((((TREESPARROW_HENAN_1_2004:0.001954008187578416,TREESPARROW_HENAN_3_2004:0.003896316686452931)Node6:0.001938506890703636,TREESPARROW_HENAN_4_2004:0)Node5:0.005890390504717593,((CHICKEN_HEBEI_326_2005:0.0118071209154035,(SWINE_ANHUI_2004:0,TREESPARROW_HENAN_2_2004:0.001939618450410721)Node13:0.01383276182388132)Node11:0.009974147725569997,((CHICKEN_HONGKONG_915_97:0,GOOSE_HONGKONG_W355_97:0)Node17:0.001941847153562197,((DUCK_HONGKONG_Y283_97:0,HONGKONG_538_97:0)Node21:0,HONGKONG_97_98:0.005840445012127324)Node20:0.001942715072940801)Node16:0.01987446960589405)Node10:0.005913850464875198)Node4:0.005886750382502456,(((DUCK_GUANGZHOU_20_2005:0.003893604042162395,GOOSE_SHANTOU_2216_2005:0.003905435534305824)Node27:0.001941929040845811,PEREGRINEFALCON_HK_D0028_2004:0.003899037680959845)Node26:0.001951590047476092,CK_HK_WF157_2003:0.005864286435734769)Node25:0.001925781157666145)Node3:0.009803928769016717,DUCK_VIETNAM_272_2005:0.01580156952635168)Node2:0,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.003890598353658968)Node1:0,((HUMAN_VIETNAM_CL105_2005:0.003905371265795895,DUCK_VIETNAM_376_2005:0.0137665342243657)Node35:0.001932867193851192,MALLARD_VIETNAM_16_2003:0.003887459835724038)Node34:0,VIETNAM_3062_2004:0.00194102772512571)"
+    },
+   "3":{
+     "bps":      [
+[1167, 1698] 
+      ],
+     "tree":"(TREESPARROW_HENAN_1_2004:0,((TREESPARROW_HENAN_3_2004:0.005713571370335148,TREESPARROW_HENAN_4_2004:0)Node3:0.00189607429178233,(CHICKEN_HEBEI_326_2005:0.005712316903324198,(SWINE_ANHUI_2004:0.005701998731046575,(((CHICKEN_HONGKONG_915_97:0,HONGKONG_97_98:0)Node12:0.001895621658683188,(GOOSE_HONGKONG_W355_97:0,HONGKONG_538_97:0)Node15:0)Node11:0.01534803500036186,((DUCK_HONGKONG_Y283_97:0.0001941011375241317,(((HUMAN_VIETNAM_CL105_2005:0.001928158212296621,DUCK_VIETNAM_376_2005:0.003824815472812549)Node23:0.001900556734363341,(VIETNAM_3062_2004:0.001945118440015516,MALLARD_VIETNAM_16_2003:0)Node26:0)Node22:0,(CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.00380825293990655,DUCK_VIETNAM_272_2005:0.005749159769097136)Node29:0.001884324589239026)Node21:0.006136201619836659)Node19:0.006956231732180768,(((DUCK_GUANGZHOU_20_2005:0.003782134609270667,GOOSE_SHANTOU_2216_2005:0.005745814969410696)Node34:0.005728903718080784,PEREGRINEFALCON_HK_D0028_2004:0)Node33:0.001883474579815808,CK_HK_WF157_2003:0.005783922057126199)Node32:0.003686703559509533)Node18:0.002359028413665987)Node10:0.003781653021946557)Node8:0.003836413220384994)Node6:0.001894177236914572)Node2:0,TREESPARROW_HENAN_2_2004:0.00767492225272676)"
+    }
+  },
+ "improvements":{
+   "0":{
+     "breakpoints":      [
+[696] 
+      ],
+     "deltaAICc":121.2176698921212
+    },
+   "1":{
+     "breakpoints":      [
+[692],
+      [1166] 
+      ],
+     "deltaAICc":51.31089620615057
+    },
+   "2":{
+     "breakpoints":      [
+[461],
+      [650],
+      [1166] 
+      ],
+     "deltaAICc":0.1679528998429305
+    }
+  },
+ "input":{
+   "file name":"/Users/ryanvelazquez/Documents/galaxy_items/tools-iuc/tools/hyphy/./test-data/gard-in1.fa",
+   "number of sequences":21,
+   "number of sites":1698,
+   "partition count":1
+  },
+ "potentialBreakpoints":244,
+ "singleTreeAICc":8952.770360670584,
+ "siteBreakPointSupport":{
+   "1005":3.828454313051127e-38,
+   "1006":3.079286891225441e-38,
+   "101":1.367441431357884e-42,
+   "1013":1.999228647805731e-38,
+   "1015":5.581552407151915e-37,
+   "1016":6.637544467285419e-30,
+   "1020":8.283127276807708e-36,
+   "1021":5.149224738126319e-36,
+   "1023":2.572721275288951e-33,
+   "1031":1.729227457250037e-39,
+   "1041":4.668316272061274e-41,
+   "1052":7.068163653642667e-45,
+   "1058":4.410408926058965e-40,
+   "1061":3.620416399436108e-31,
+   "1070":1.30023862441172e-32,
+   "1073":2.392244771912456e-29,
+   "108":1.088323481504585e-09,
+   "1082":1.781042369034824e-32,
+   "1085":1.072215721126058e-30,
+   "1106":8.711808244586844e-32,
+   "1124":2.066632617058007e-32,
+   "1130":2.365201133574919e-32,
+   "1136":1.180024224431614e-32,
+   "1149":2.0594328664778e-30,
+   "116":3.062613098803733e-06,
+   "1166":1.382998480016903e-28,
+   "1206":4.271112529885021e-30,
+   "1223":2.439400027544238e-30,
+   "1250":2.1846050762587e-31,
+   "1271":1.963370249731928e-32,
+   "1286":1.143587697307953e-32,
+   "1292":1.940620880105886e-32,
+   "1298":1.19984441620646e-32,
+   "1319":5.201055420999954e-33,
+   "1322":1.490898155414118e-32,
+   "1334":6.386384600277327e-33,
+   "134":7.744769428033727e-17,
+   "1361":2.822486839844269e-33,
+   "1384":1.557822413676087e-33,
+   "1397":1.068642031138833e-35,
+   "1412":6.831611952947673e-38,
+   "1418":1.522690852126543e-39,
+   "1430":7.96352395927298e-40,
+   "1433":1.156793517215151e-37,
+   "1436":5.651778976453802e-38,
+   "144":8.552230281908163e-07,
+   "1442":2.016530452321108e-37,
+   "1454":2.386567702095966e-36,
+   "1463":9.043007916183422e-39,
+   "1465":7.669880260535686e-39,
+   "1473":3.675784601460829e-36,
+   "1481":2.661546849207671e-37,
+   "149":1.304259029589306e-05,
+   "1495":4.622941797307467e-44,
+   "1496":4.226996151791482e-44,
+   "1499":2.730615034063184e-44,
+   "151":1.790975065283929e-08,
+   "1515":4.749012537570416e-45,
+   "1516":1.058313486583168e-45,
+   "1519":3.729412022561233e-46,
+   "1520":2.407045351616036e-46,
+   "1521":1.689577693820857e-46,
+   "1523":5.07686612591507e-46,
+   "1524":1.741238756038766e-46,
+   "1526":3.855324589536673e-46,
+   "1537":2.062102436942228e-46,
+   "1538":3.417841619348906e-47,
+   "1539":3.047730711305713e-47,
+   "1544":1.7639941893744e-47,
+   "155":1.315748190900565e-29,
+   "1556":1.89572005098281e-47,
+   "1580":5.505818788734445e-49,
+   "1585":1.614020745294316e-49,
+   "159":2.814745521856487e-30,
+   "161":5.278607654454491e-08,
+   "1610":6.983674612335563e-50,
+   "1613":1.219959907173526e-49,
+   "1616":1.379005387331829e-49,
+   "1618":1.403866743396411e-51,
+   "1619":6.05913881499244e-52,
+   "1631":1.563107434100785e-52,
+   "1632":5.045949522041951e-52,
+   "1644":1.457045566204417e-52,
+   "1646":1.817307863422175e-52,
+   "1658":2.336582715408929e-53,
+   "173":3.057688318766887e-09,
+   "174":3.878560193985558e-09,
+   "176":8.37052095471109e-08,
+   "177":1.79882740520206e-07,
+   "178":4.189275930585918e-07,
+   "180":3.648108711445327e-07,
+   "185":8.602578155282706e-07,
+   "191":2.146033440200939e-05,
+   "197":1.254742955877914e-07,
+   "203":1.782085063210574e-09,
+   "205":3.9041258553037e-08,
+   "206":6.68882932678853e-21,
+   "209":6.086107365200133e-07,
+   "218":3.339578115382376e-06,
+   "230":4.417475117693213e-07,
+   "233":5.355261458449197e-05,
+   "236":0.007922604577960988,
+   "239":0.001674452816751232,
+   "242":0.003084865524315277,
+   "251":0.001911517032820398,
+   "257":0.001206425464437376,
+   "266":0.0006256067585931275,
+   "272":0.0004205386287599137,
+   "295":0.0006020604873750697,
+   "298":7.88207661427839e-10,
+   "303":1.196432870877656e-11,
+   "304":4.034129303399593e-10,
+   "310":1.00120863585874e-18,
+   "320":9.255079503229926e-08,
+   "326":1.316695923941227e-11,
+   "327":9.749462853855344e-30,
+   "328":5.468914334726157e-06,
+   "335":5.399829244004923e-09,
+   "336":1.259324706217958e-11,
+   "338":4.933684745749596e-07,
+   "348":4.415481383174255e-09,
+   "383":1.208370214471027e-18,
+   "391":4.182822911348255e-18,
+   "407":6.023041146737167e-09,
+   "414":5.844791249373782e-06,
+   "417":1.35252270798266e-09,
+   "418":0.0002946717374488142,
+   "419":2.325837885934838e-10,
+   "424":1.929854665115397e-05,
+   "425":8.20012614644675e-05,
+   "426":4.822853182787663e-05,
+   "433":0.001868063738600832,
+   "437":3.538850116792625e-27,
+   "440":0.08010977685280053,
+   "448":0.07606312788914485,
+   "45":5.811735655101648e-16,
+   "453":0.03671194147765044,
+   "455":0.02091509793683489,
+   "458":0.07150971750425916,
+   "460":0.7998321443046799,
+   "461":1,
+   "464":0.001724550519344097,
+   "466":0.0008356143264203861,
+   "467":1.657561796358788e-05,
+   "468":1.348444812921266e-23,
+   "498":1.148320825350936e-24,
+   "50":8.32428744865e-23,
+   "509":1.189408841111924e-08,
+   "511":2.022119078897978e-24,
+   "513":3.201599896136264e-07,
+   "518":2.988923843741992e-13,
+   "522":2.646016563727863e-07,
+   "524":2.999275395428511e-07,
+   "531":7.048583824652365e-06,
+   "532":8.871326441721272e-07,
+   "534":0.008873756999646102,
+   "535":0.004214591771216962,
+   "542":0.08914224508165824,
+   "553":7.90490584470731e-05,
+   "57":2.385720839099584e-24,
+   "570":9.913916137860915e-09,
+   "572":4.275862281976158e-10,
+   "584":3.314094298879245e-10,
+   "587":3.973343100406481e-07,
+   "590":4.873195666004712e-11,
+   "598":6.298174788936176e-09,
+   "60":1.133242133399893e-14,
+   "600":7.913894896186118e-20,
+   "61":2.995574404290199e-12,
+   "610":4.210551218094785e-06,
+   "615":9.779938062686411e-06,
+   "617":3.115657726300164e-05,
+   "626":1.626356028661979e-05,
+   "631":1.964642052027623e-05,
+   "635":2.944226387161727e-05,
+   "638":3.016399268517012e-06,
+   "639":2.178996517448726e-17,
+   "650":7.796278074051867e-11,
+   "662":8.522743624982774e-11,
+   "665":2.026783501294749e-13,
+   "671":1.546378067090648e-12,
+   "675":0.002961528524188881,
+   "677":2.552472267524399e-10,
+   "681":0.02600692507802804,
+   "682":0.005058690616537698,
+   "689":2.914183309131261e-06,
+   "692":0.3722918462191203,
+   "696":0.002394988564901264,
+   "702":0.1907562583825546,
+   "707":1.690629082138237e-08,
+   "710":7.270598199039235e-12,
+   "719":1.193577032271698e-24,
+   "722":6.242541477357492e-12,
+   "725":2.246819705265767e-24,
+   "749":1.075902126658883e-29,
+   "75":1.958058873662239e-39,
+   "758":1.862151711463288e-23,
+   "759":5.809642307223274e-30,
+   "761":7.82644516929739e-23,
+   "767":6.985390677891108e-34,
+   "773":1.159688507258433e-33,
+   "78":8.369563434460729e-21,
+   "794":2.615288564009047e-34,
+   "803":3.007434714722189e-27,
+   "810":6.65516462801252e-34,
+   "812":2.065239894547715e-33,
+   "83":1.903013516419069e-15,
+   "833":1.55354314155857e-30,
+   "834":5.458420523940027e-37,
+   "836":1.227693373364261e-29,
+   "845":2.516382791081784e-31,
+   "848":5.804977376214689e-37,
+   "863":2.868441667452538e-42,
+   "872":1.784676508419814e-43,
+   "878":2.0081213960433e-43,
+   "887":1.13493422288884e-43,
+   "891":1.700300743179312e-36,
+   "905":1.109981525417329e-42,
+   "911":2.50641030292061e-44,
+   "917":1.208124588626152e-44,
+   "926":5.840308910078806e-45,
+   "932":2.793211015138247e-45,
+   "935":4.67970437488018e-44,
+   "94":9.387247404190512e-24,
+   "942":6.30144926979359e-44,
+   "950":3.018547209001381e-44,
+   "978":2.723057526622017e-45,
+   "98":2.547710617920883e-27,
+   "983":2.72991889467319e-45,
+   "986":6.142043558494514e-45,
+   "992":1.349612353859241e-47,
+   "995":3.874956487042822e-49
+  },
+ "timeElapsed":1045,
+ "totalModelCount":4369,
+ "trees":{
+   "0":{
+     "newickString":"(((((((TREESPARROW_HENAN_1_2004:0.01973996359641645,TREESPARROW_HENAN_2_2004:0)Node6:0.006601594605919903,CHICKEN_HEBEI_326_2005:0.02877904543700591)Node5:0.002960697265622527,SWINE_ANHUI_2004:0.01220336915594569)Node4:0.004301817483024902,((DUCK_GUANGZHOU_20_2005:0.006496379151101181,(GOOSE_SHANTOU_2216_2005:0.008666763019733412,PEREGRINEFALCON_HK_D0028_2004:0.006494907750172948)Node14:0)Node12:0.006529386248252737,CK_HK_WF157_2003:0.008749819170042668)Node11:0.006517868346508392)Node3:0.004369843971142481,((TREESPARROW_HENAN_3_2004:0.004310725480928182,((CHICKEN_HONGKONG_915_97:0,(HONGKONG_97_98:0.007234718327388172,HONGKONG_538_97:0)Node24:0)Node22:0,(GOOSE_HONGKONG_W355_97:0,DUCK_HONGKONG_Y283_97:0)Node27:0.002160209380619512)Node21:0.02651640051975179)Node19:0.002209468499615626,TREESPARROW_HENAN_4_2004:0.008707376458939551)Node18:0)Node2:0.01527162191938894,MALLARD_VIETNAM_16_2003:0.00216300836609909)Node1:0,HUMAN_VIETNAM_CL105_2005:0.01089634139979296,(((DUCK_VIETNAM_376_2005:0.002165747961920766,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.01092964139649115)Node35:0.002165571630784742,VIETNAM_3062_2004:0)Node34:0.002160659783816526,DUCK_VIETNAM_272_2005:0.006501625005083654)Node33:0)"
+    },
+   "1":{
+     "newickString":"((((((TREESPARROW_HENAN_1_2004:0,TREESPARROW_HENAN_3_2004:0.01064277225673711)Node5:0.00531987705161906,TREESPARROW_HENAN_2_2004:0)Node4:0.005231591103466107,CHICKEN_HEBEI_326_2005:0.05043188754547531)Node3:0.005435427857192481,CK_HK_WF157_2003:0)Node2:0.005367407450692448,((TREESPARROW_HENAN_4_2004:0.005403333058615208,(((CHICKEN_HONGKONG_915_97:0,(GOOSE_HONGKONG_W355_97:0,DUCK_HONGKONG_Y283_97:0)Node18:0.005303893633648769)Node16:0,HONGKONG_97_98:0)Node15:0,HONGKONG_538_97:0)Node14:0.0160450339521957)Node12:0.01065583332597595,((DUCK_GUANGZHOU_20_2005:0.02156617952480121,GOOSE_SHANTOU_2216_2005:0.005315754078746889)Node24:0,PEREGRINEFALCON_HK_D0028_2004:0.005310132566451705)Node23:0)Node11:0.005324661683629481)Node1:0.01075596871747344,(SWINE_ANHUI_2004:0.01612941661930485,DUCK_VIETNAM_272_2005:0.005332918418299072)Node28:0.005343017103483476,((HUMAN_VIETNAM_CL105_2005:0.01615610619083483,DUCK_VIETNAM_376_2005:0.01622595235090508)Node32:0.005403715853761346,(VIETNAM_3062_2004:0,(MALLARD_VIETNAM_16_2003:0.01066500623689393,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0)Node37:0.005316372444723995)Node35:0)Node31:0)"
+    },
+   "2":{
+     "newickString":"(((((((TREESPARROW_HENAN_1_2004:0.001954008187578416,TREESPARROW_HENAN_3_2004:0.003896316686452931)Node6:0.001938506890703636,TREESPARROW_HENAN_4_2004:0)Node5:0.005890390504717593,((CHICKEN_HEBEI_326_2005:0.0118071209154035,(SWINE_ANHUI_2004:0,TREESPARROW_HENAN_2_2004:0.001939618450410721)Node13:0.01383276182388132)Node11:0.009974147725569997,((CHICKEN_HONGKONG_915_97:0,GOOSE_HONGKONG_W355_97:0)Node17:0.001941847153562197,((DUCK_HONGKONG_Y283_97:0,HONGKONG_538_97:0)Node21:0,HONGKONG_97_98:0.005840445012127324)Node20:0.001942715072940801)Node16:0.01987446960589405)Node10:0.005913850464875198)Node4:0.005886750382502456,(((DUCK_GUANGZHOU_20_2005:0.003893604042162395,GOOSE_SHANTOU_2216_2005:0.003905435534305824)Node27:0.001941929040845811,PEREGRINEFALCON_HK_D0028_2004:0.003899037680959845)Node26:0.001951590047476092,CK_HK_WF157_2003:0.005864286435734769)Node25:0.001925781157666145)Node3:0.009803928769016717,DUCK_VIETNAM_272_2005:0.01580156952635168)Node2:0,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.003890598353658968)Node1:0,((HUMAN_VIETNAM_CL105_2005:0.003905371265795895,DUCK_VIETNAM_376_2005:0.0137665342243657)Node35:0.001932867193851192,MALLARD_VIETNAM_16_2003:0.003887459835724038)Node34:0,VIETNAM_3062_2004:0.00194102772512571)"
+    },
+   "3":{
+     "newickString":"(TREESPARROW_HENAN_1_2004:0,((TREESPARROW_HENAN_3_2004:0.005713571370335148,TREESPARROW_HENAN_4_2004:0)Node3:0.00189607429178233,(CHICKEN_HEBEI_326_2005:0.005712316903324198,(SWINE_ANHUI_2004:0.005701998731046575,(((CHICKEN_HONGKONG_915_97:0,HONGKONG_97_98:0)Node12:0.001895621658683188,(GOOSE_HONGKONG_W355_97:0,HONGKONG_538_97:0)Node15:0)Node11:0.01534803500036186,((DUCK_HONGKONG_Y283_97:0.0001941011375241317,(((HUMAN_VIETNAM_CL105_2005:0.001928158212296621,DUCK_VIETNAM_376_2005:0.003824815472812549)Node23:0.001900556734363341,(VIETNAM_3062_2004:0.001945118440015516,MALLARD_VIETNAM_16_2003:0)Node26:0)Node22:0,(CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.00380825293990655,DUCK_VIETNAM_272_2005:0.005749159769097136)Node29:0.001884324589239026)Node21:0.006136201619836659)Node19:0.006956231732180768,(((DUCK_GUANGZHOU_20_2005:0.003782134609270667,GOOSE_SHANTOU_2216_2005:0.005745814969410696)Node34:0.005728903718080784,PEREGRINEFALCON_HK_D0028_2004:0)Node33:0.001883474579815808,CK_HK_WF157_2003:0.005783922057126199)Node32:0.003686703559509533)Node18:0.002359028413665987)Node10:0.003781653021946557)Node8:0.003836413220384994)Node6:0.001894177236914572)Node2:0,TREESPARROW_HENAN_2_2004:0.00767492225272676)"
+    }
+  }
+}
\ No newline at end of file