Mercurial > repos > iuc > hyphy_meme

comparison test-data/gard-out1.json @ 25:e0763df98352 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 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author iuc
date Tue, 27 Apr 2021 17:59:28 +0000
parents 7b3f9c78cf6d
children
comparison
equal deleted inserted replaced
24:efdd06f7f857 25:e0763df98352
1 { 1 {
2 "analysis":{ 2 "analysis":{
3 "authors":"Sergei L Kosakovsky Pond", 3 "authors":"Sergei L Kosakovsky Pond",
4 "citation":"**Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm**, _Mol Biol Evol 23(10), 1891–1901", 4 "citation":"**Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm**, _Mol Biol Evol 23(10), 1891–1901",
5 "contact":"spond@temple.edu", 5 "contact":"spond@temple.edu",
6 "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.", 6 "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. v0.2 adds and spooling results to JSON after each breakpoint search conclusion",
7 "requirements":"A sequence alignment.", 7 "requirements":"A sequence alignment.",
8 "version":"0.1" 8 "version":"0.2"
9 }, 9 },
10 "baselineScore":8884.998566352424, 10 "baselineScore":1450.968340148184,
11 "bestModelAICc":1450.968340148184,
11 "breakpointData":{ 12 "breakpointData":{
12 "0":{ 13 "bps": [
13 "bps": [ 14 [1, 428]
14 [1, 461] 15 ],
15 ], 16 "tree":"((BRO1_1:0,BRO2:0.007408926175080497)Node1:0,(BRO3_1:0.002455524404855022,BRO4:0.002457415365886074)Node4:0,(((BRO5:0.002464479112430666,(BRO6:0.004940850926103086,BRO7_1:0)Node11:0)Node9:0.002460542727794925,(BRO9:0.004931390913247289,((BRO10:0.002933649980980302,BRO11_1:0.01453409151831228)Node17:0.002436921831192641,BRO12:0.006987081661112447)Node16:0.005417113782285573)Node14:0)Node8:0,BRO8:0.002462026756884335)Node7:0)"
16 "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)"
17 },
18 "1":{
19 "bps": [
20 [462, 650]
21 ],
22 "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)"
23 },
24 "2":{
25 "bps": [
26 [651, 1166]
27 ],
28 "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)"
29 },
30 "3":{
31 "bps": [
32 [1167, 1698]
33 ],
34 "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)"
35 }
36 },
37 "improvements":{
38 "0":{
39 "breakpoints": [
40 [696]
41 ],
42 "deltaAICc":121.2176698921212
43 },
44 "1":{
45 "breakpoints": [
46 [692],
47 [1166]
48 ],
49 "deltaAICc":51.31089620615057
50 },
51 "2":{
52 "breakpoints": [
53 [461],
54 [650],
55 [1166]
56 ],
57 "deltaAICc":0.1679528998429305
58 }
59 }, 17 },
60 "input":{ 18 "input":{
61 "file name":"/Users/ryanvelazquez/Documents/galaxy_items/tools-iuc/tools/hyphy/./test-data/gard-in1.fa", 19 "file name":"/tmp/tmpht3ax8lq/job_working_directory/000/2/working/./input.fasta",
62 "number of sequences":21, 20 "number of sequences":12,
63 "number of sites":1698, 21 "number of sites":428,
64 "partition count":1 22 "partition count":1
65 }, 23 },
66 "potentialBreakpoints":244, 24 "potentialBreakpoints":21,
67 "singleTreeAICc":8952.770360670584, 25 "singleTreeAICc":1450.968340686507,
68 "siteBreakPointSupport":{ 26 "siteBreakPointSupport":{
69 "1005":3.828454313051127e-38, 27 "130":7.71938316947624e-08,
70 "1006":3.079286891225441e-38, 28 "150":7.49872016582054e-06,
71 "101":1.367441431357884e-42, 29 "158":4.898720800158644e-06,
72 "1013":1.999228647805731e-38, 30 "175":0.0001152764571690805,
73 "1015":5.581552407151915e-37, 31 "176":0.000624401895637527,
74 "1016":6.637544467285419e-30, 32 "183":8.845949780426112e-06,
75 "1020":8.283127276807708e-36, 33 "196":5.17454230945286e-06,
76 "1021":5.149224738126319e-36, 34 "197":5.9168232845333e-06,
77 "1023":2.572721275288951e-33, 35 "198":4.436819044306368e-05,
78 "1031":1.729227457250037e-39, 36 "227":2.830236103715775e-06,
79 "1041":4.668316272061274e-41, 37 "233":9.74236872039044e-06,
80 "1052":7.068163653642667e-45, 38 "241":1.802640814372882e-05,
81 "1058":4.410408926058965e-40, 39 "245":1.305334911931824e-05,
82 "1061":3.620416399436108e-31, 40 "252":8.580180939514955e-06,
83 "1070":1.30023862441172e-32, 41 "253":2.317805781298633e-05,
84 "1073":2.392244771912456e-29, 42 "260":1.77855732841814e-06,
85 "108":1.088323481504585e-09, 43 "287":4.449903505856628e-07,
86 "1082":1.781042369034824e-32, 44 "325":6.636014843884652e-09,
87 "1085":1.072215721126058e-30, 45 "326":2.134836027957093e-09,
88 "1106":8.711808244586844e-32, 46 "334":7.302354343864046e-09,
89 "1124":2.066632617058007e-32, 47 "341":1.678880851117679e-09,
90 "1130":2.365201133574919e-32, 48 "358":6.863087158511391e-14
91 "1136":1.180024224431614e-32,
92 "1149":2.0594328664778e-30,
93 "116":3.062613098803733e-06,
94 "1166":1.382998480016903e-28,
95 "1206":4.271112529885021e-30,
96 "1223":2.439400027544238e-30,
97 "1250":2.1846050762587e-31,
98 "1271":1.963370249731928e-32,
99 "1286":1.143587697307953e-32,
100 "1292":1.940620880105886e-32,
101 "1298":1.19984441620646e-32,
102 "1319":5.201055420999954e-33,
103 "1322":1.490898155414118e-32,
104 "1334":6.386384600277327e-33,
105 "134":7.744769428033727e-17,
106 "1361":2.822486839844269e-33,
107 "1384":1.557822413676087e-33,
108 "1397":1.068642031138833e-35,
109 "1412":6.831611952947673e-38,
110 "1418":1.522690852126543e-39,
111 "1430":7.96352395927298e-40,
112 "1433":1.156793517215151e-37,
113 "1436":5.651778976453802e-38,
114 "144":8.552230281908163e-07,
115 "1442":2.016530452321108e-37,
116 "1454":2.386567702095966e-36,
117 "1463":9.043007916183422e-39,
118 "1465":7.669880260535686e-39,
119 "1473":3.675784601460829e-36,
120 "1481":2.661546849207671e-37,
121 "149":1.304259029589306e-05,
122 "1495":4.622941797307467e-44,
123 "1496":4.226996151791482e-44,
124 "1499":2.730615034063184e-44,
125 "151":1.790975065283929e-08,
126 "1515":4.749012537570416e-45,
127 "1516":1.058313486583168e-45,
128 "1519":3.729412022561233e-46,
129 "1520":2.407045351616036e-46,
130 "1521":1.689577693820857e-46,
131 "1523":5.07686612591507e-46,
132 "1524":1.741238756038766e-46,
133 "1526":3.855324589536673e-46,
134 "1537":2.062102436942228e-46,
135 "1538":3.417841619348906e-47,
136 "1539":3.047730711305713e-47,
137 "1544":1.7639941893744e-47,
138 "155":1.315748190900565e-29,
139 "1556":1.89572005098281e-47,
140 "1580":5.505818788734445e-49,
141 "1585":1.614020745294316e-49,
142 "159":2.814745521856487e-30,
143 "161":5.278607654454491e-08,
144 "1610":6.983674612335563e-50,
145 "1613":1.219959907173526e-49,
146 "1616":1.379005387331829e-49,
147 "1618":1.403866743396411e-51,
148 "1619":6.05913881499244e-52,
149 "1631":1.563107434100785e-52,
150 "1632":5.045949522041951e-52,
151 "1644":1.457045566204417e-52,
152 "1646":1.817307863422175e-52,
153 "1658":2.336582715408929e-53,
154 "173":3.057688318766887e-09,
155 "174":3.878560193985558e-09,
156 "176":8.37052095471109e-08,
157 "177":1.79882740520206e-07,
158 "178":4.189275930585918e-07,
159 "180":3.648108711445327e-07,
160 "185":8.602578155282706e-07,
161 "191":2.146033440200939e-05,
162 "197":1.254742955877914e-07,
163 "203":1.782085063210574e-09,
164 "205":3.9041258553037e-08,
165 "206":6.68882932678853e-21,
166 "209":6.086107365200133e-07,
167 "218":3.339578115382376e-06,
168 "230":4.417475117693213e-07,
169 "233":5.355261458449197e-05,
170 "236":0.007922604577960988,
171 "239":0.001674452816751232,
172 "242":0.003084865524315277,
173 "251":0.001911517032820398,
174 "257":0.001206425464437376,
175 "266":0.0006256067585931275,
176 "272":0.0004205386287599137,
177 "295":0.0006020604873750697,
178 "298":7.88207661427839e-10,
179 "303":1.196432870877656e-11,
180 "304":4.034129303399593e-10,
181 "310":1.00120863585874e-18,
182 "320":9.255079503229926e-08,
183 "326":1.316695923941227e-11,
184 "327":9.749462853855344e-30,
185 "328":5.468914334726157e-06,
186 "335":5.399829244004923e-09,
187 "336":1.259324706217958e-11,
188 "338":4.933684745749596e-07,
189 "348":4.415481383174255e-09,
190 "383":1.208370214471027e-18,
191 "391":4.182822911348255e-18,
192 "407":6.023041146737167e-09,
193 "414":5.844791249373782e-06,
194 "417":1.35252270798266e-09,
195 "418":0.0002946717374488142,
196 "419":2.325837885934838e-10,
197 "424":1.929854665115397e-05,
198 "425":8.20012614644675e-05,
199 "426":4.822853182787663e-05,
200 "433":0.001868063738600832,
201 "437":3.538850116792625e-27,
202 "440":0.08010977685280053,
203 "448":0.07606312788914485,
204 "45":5.811735655101648e-16,
205 "453":0.03671194147765044,
206 "455":0.02091509793683489,
207 "458":0.07150971750425916,
208 "460":0.7998321443046799,
209 "461":1,
210 "464":0.001724550519344097,
211 "466":0.0008356143264203861,
212 "467":1.657561796358788e-05,
213 "468":1.348444812921266e-23,
214 "498":1.148320825350936e-24,
215 "50":8.32428744865e-23,
216 "509":1.189408841111924e-08,
217 "511":2.022119078897978e-24,
218 "513":3.201599896136264e-07,
219 "518":2.988923843741992e-13,
220 "522":2.646016563727863e-07,
221 "524":2.999275395428511e-07,
222 "531":7.048583824652365e-06,
223 "532":8.871326441721272e-07,
224 "534":0.008873756999646102,
225 "535":0.004214591771216962,
226 "542":0.08914224508165824,
227 "553":7.90490584470731e-05,
228 "57":2.385720839099584e-24,
229 "570":9.913916137860915e-09,
230 "572":4.275862281976158e-10,
231 "584":3.314094298879245e-10,
232 "587":3.973343100406481e-07,
233 "590":4.873195666004712e-11,
234 "598":6.298174788936176e-09,
235 "60":1.133242133399893e-14,
236 "600":7.913894896186118e-20,
237 "61":2.995574404290199e-12,
238 "610":4.210551218094785e-06,
239 "615":9.779938062686411e-06,
240 "617":3.115657726300164e-05,
241 "626":1.626356028661979e-05,
242 "631":1.964642052027623e-05,
243 "635":2.944226387161727e-05,
244 "638":3.016399268517012e-06,
245 "639":2.178996517448726e-17,
246 "650":7.796278074051867e-11,
247 "662":8.522743624982774e-11,
248 "665":2.026783501294749e-13,
249 "671":1.546378067090648e-12,
250 "675":0.002961528524188881,
251 "677":2.552472267524399e-10,
252 "681":0.02600692507802804,
253 "682":0.005058690616537698,
254 "689":2.914183309131261e-06,
255 "692":0.3722918462191203,
256 "696":0.002394988564901264,
257 "702":0.1907562583825546,
258 "707":1.690629082138237e-08,
259 "710":7.270598199039235e-12,
260 "719":1.193577032271698e-24,
261 "722":6.242541477357492e-12,
262 "725":2.246819705265767e-24,
263 "749":1.075902126658883e-29,
264 "75":1.958058873662239e-39,
265 "758":1.862151711463288e-23,
266 "759":5.809642307223274e-30,
267 "761":7.82644516929739e-23,
268 "767":6.985390677891108e-34,
269 "773":1.159688507258433e-33,
270 "78":8.369563434460729e-21,
271 "794":2.615288564009047e-34,
272 "803":3.007434714722189e-27,
273 "810":6.65516462801252e-34,
274 "812":2.065239894547715e-33,
275 "83":1.903013516419069e-15,
276 "833":1.55354314155857e-30,
277 "834":5.458420523940027e-37,
278 "836":1.227693373364261e-29,
279 "845":2.516382791081784e-31,
280 "848":5.804977376214689e-37,
281 "863":2.868441667452538e-42,
282 "872":1.784676508419814e-43,
283 "878":2.0081213960433e-43,
284 "887":1.13493422288884e-43,
285 "891":1.700300743179312e-36,
286 "905":1.109981525417329e-42,
287 "911":2.50641030292061e-44,
288 "917":1.208124588626152e-44,
289 "926":5.840308910078806e-45,
290 "932":2.793211015138247e-45,
291 "935":4.67970437488018e-44,
292 "94":9.387247404190512e-24,
293 "942":6.30144926979359e-44,
294 "950":3.018547209001381e-44,
295 "978":2.723057526622017e-45,
296 "98":2.547710617920883e-27,
297 "983":2.72991889467319e-45,
298 "986":6.142043558494514e-45,
299 "992":1.349612353859241e-47,
300 "995":3.874956487042822e-49
301 }, 49 },
302 "timeElapsed":1045, 50 "timeElapsed":8,
303 "totalModelCount":4369, 51 "totalModelCount":209,
304 "trees":{ 52 "trees":{
305 "0":{ 53 "newickString":"((BRO1_1:0,BRO2:0.007408926175080497)Node1:0,(BRO3_1:0.002455524404855022,BRO4:0.002457415365886074)Node4:0,(((BRO5:0.002464479112430666,(BRO6:0.004940850926103086,BRO7_1:0)Node11:0)Node9:0.002460542727794925,(BRO9:0.004931390913247289,((BRO10:0.002933649980980302,BRO11_1:0.01453409151831228)Node17:0.002436921831192641,BRO12:0.006987081661112447)Node16:0.005417113782285573)Node14:0)Node8:0,BRO8:0.002462026756884335)Node7:0)"
306 "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)"
307 },
308 "1":{
309 "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)"
310 },
311 "2":{
312 "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)"
313 },
314 "3":{
315 "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)"
316 }
317 } 54 }
318 } 55 }