| Previous changeset 1:b678fe748dc5 (2019-08-21) Next changeset 3:1d8b63d18f30 (2020-02-14) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798" |
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modified:
hyphy_busted.xml macros.xml test-data/bgm-out1.json test-data/busted-out1.json test-data/gard-out1.nex |
| b |
| diff -r b678fe748dc5 -r f8d88dcef64e hyphy_busted.xml --- a/hyphy_busted.xml Wed Aug 21 12:22:30 2019 -0400 +++ b/hyphy_busted.xml Thu Feb 13 15:00:14 2020 -0500 |
| [ |
| @@ -33,6 +33,10 @@ </tests> <help><![CDATA[ BUSTED will test for gene-wide selection at pre-specified lineages. This method is particularly useful for relatively small datasets (fewer than 10 taxa) where other methods may not have sufficient power to detect selection. This method is not suitable for identifying specific sites subject to positive selection. + +See the online documentation_ for more information. + +.. _documentation: http://hyphy.org/methods/selection-methods/#busted ]]></help> <expand macro="citations"> <citation type="doi">10.1093/molbev/msv035</citation> |
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| diff -r b678fe748dc5 -r f8d88dcef64e macros.xml --- a/macros.xml Wed Aug 21 12:22:30 2019 -0400 +++ b/macros.xml Thu Feb 13 15:00:14 2020 -0500 |
| b |
| @@ -72,7 +72,7 @@ <yield/> </citations> </xml> - <token name="@VERSION@">2.5.0</token> + <token name="@VERSION@">2.5.2</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@"> |
| b |
| diff -r b678fe748dc5 -r f8d88dcef64e test-data/bgm-out1.json --- a/test-data/bgm-out1.json Wed Aug 21 12:22:30 2019 -0400 +++ b/test-data/bgm-out1.json Thu Feb 13 15:00:14 2020 -0500 |
| [ |
| b'@@ -1,282 +1,42 @@\n {\n "MLE":{\n "content": [\n-[3, 4, 0.01806536842133838, 0.0196151052739404, 0.03768047369527878, 2, 4, 1],\n- [3, 5, 0.0136689326165866, 0.08411879896894461, 0.09778773158553121, 2, 2, 1],\n- [3, 6, 0.01626880980001384, 0.05621779910581199, 0.07248660890582583, 2, 2, 1],\n- [3, 7, 0.01296085994820069, 0.02206081801264715, 0.03502167796084783, 2, 1, 0],\n- [3, 9, 0.01069476203525126, 0.01376808584576788, 0.02446284788101914, 2, 3, 0],\n- [3, 10, 0.05465425513197631, 0.1433115560788012, 0.1979658112107776, 2, 1, 1],\n- [3, 11, 0.02893963856420952, 0.01605584764833427, 0.04499548621254379, 2, 1, 0],\n- [3, 12, 0.01072516405613842, 0.0249434485528662, 0.03566861260900463, 2, 1, 0],\n- [3, 14, 0.02105948857071199, 0.05408645518169206, 0.07514594375240405, 2, 2, 1],\n- [3, 15, 0.0123000231875007, 0.02432900062064017, 0.03662902380814088, 2, 3, 1],\n- [3, 16, 0.005326227185235535, 0.02715178476956077, 0.0324780119547963, 2, 4, 1],\n- [3, 17, 0.03377277022598092, 0.04443847194728315, 0.07821124217326408, 2, 2, 1],\n- [3, 18, 0.01498654024671119, 0.01399705284721538, 0.02898359309392656, 2, 2, 0],\n- [3, 20, 0.03160117895292701, 0.03379356385898681, 0.06539474281191382, 2, 3, 1],\n- [3, 21, 0.005825814343840907, 0.01762290041418722, 0.02344871475802813, 2, 5, 1],\n- [3, 22, 0.004808842565391303, 0.01857986311191453, 0.02338870567730583, 2, 5, 1],\n- [3, 23, 0.01560225549428971, 0.01369335589628938, 0.02929561139057909, 2, 3, 0],\n- [3, 24, 0.02796792379060828, 0.0120172661798151, 0.03998518997042338, 2, 2, 0],\n- [3, 25, 0.004879890854338218, 0.05174659736268138, 0.05662648821701959, 2, 3, 1],\n- [3, 26, 0.008542556433088364, 0.02342067235707167, 0.03196322879016003, 2, 1, 0],\n- [3, 28, 0.02842598870361674, 0.04882702442678508, 0.07725301313040182, 2, 2, 1],\n- [3, 29, 0.02983611705240465, 0.04834281650968934, 0.07817893356209399, 2, 2, 1],\n- [3, 30, 0.02136530753356511, 0.056551049600131, 0.0779163571336961, 2, 2, 1],\n- [4, 5, 0.04128639081201998, 0.1643521228119713, 0.2056385136239913, 4, 2, 2],\n- [4, 6, 0.002891680521324363, 0.02014100082658794, 0.0230326813479123, 4, 2, 1],\n- [4, 7, 0.01937071123900217, 0.03955420345740617, 0.05892491469640834, 4, 1, 1],\n- [4, 9, 0.005876622911646858, 0.01316366694762399, 0.01904028985927084, 4, 3, 1],\n- [4, 10, 0.02063883956421052, 0.03235708509290364, 0.05299592465711416, 4, 1, 1],\n- [4, 11, 0.05646705485150577, 0.03046422064113512, 0.08693127549264089, 4, 1, 1],\n- [4, 12, 0.018550325874111, 0.04456585108483763, 0.06311617695894862, 4, 1, 1],\n- [4, 14, 0.002644483178150749, 0.02400887432195999, 0.02665335750011074, 4, 2, 1],\n- [4, 15, 0.01378625971212575, 0.03709407143284885, 0.05088033114497461, 4, 3, 2],\n- [4, 16, 0.005366210549264398, 0.0254419855729714, 0.03080819612223579, 4, 4, 2],\n- [4, 17, 0.08506807888824773, 0.08873474434715359, 0.1738028232354013, 4, 2, 2],\n- [4, 18, 0.01666065271395927, 0.01550783907099662, 0.03216849178495589, 4, 2, 1],\n- [4, 20, 0.0602710511807769, 0.03562465630098035, 0.09589570748175724, 4, 3, 2],\n- [4, 21, 0.03064565490801606, 0.06355132795273535, 0.09419698286075141, 4, 5, 3],\n- [4, 22, 0.02451199601165472, 0.07489768093572295, 0.09940967694737768, 4, 5, 3],\n- [4, 23, 0.03630394203907011, 0.03058821944652209, 0.06689216148559221, 4, 3, 2],\n- [4, 24, 0.02164778178638001, 0.008961778863845419, 0.03060956065022543, 4, 2, 0],\n- [4, 25, 0.01168690527839325, 0.07747501344981376, 0.08916191872820702, 4, 3, 2],\n- [4, 26, 0.01588288283660194, 0.04096522221306678, 0.05684810504966872, 4, 1, 1],\n- [4, 28, 0.01128665086452497, 0.01582662360389917, 0.02711327446842414, 4, 2, 1],\n- [4, 29, 0.01028593387764938, 0.01547886135935664, 0.02576479523700602, 4, 2, 1],\n- [4, 30, 0.004517730197507495, 0.02179721676324585, 0.02631494696075334, 4, 2, 1],\n- [5, 6, 0.01349845941886215, 0.0271001713778612, 0.04059863079672335, 2, 2, 1],\n- [5, 7, 0.'..b'cription":0.7933191636859576\n+ "models.codon.MG_REV.ModelDescription":0.8288168941011919\n },\n "Chimp":{\n- "models.DNA.GTR.ModelDescription":0\n+ "models.codon.MG_REV.ModelDescription":0\n },\n "Cow":{\n- "models.DNA.GTR.ModelDescription":0.8094119333244753\n+ "models.codon.MG_REV.ModelDescription":0.8164924147537205\n },\n "Horse":{\n- "models.DNA.GTR.ModelDescription":0.2769077630163064\n+ "models.codon.MG_REV.ModelDescription":0.2841592907567805\n },\n "Human":{\n- "models.DNA.GTR.ModelDescription":0\n+ "models.codon.MG_REV.ModelDescription":0\n },\n "Mouse":{\n- "models.DNA.GTR.ModelDescription":0.1094921058577506\n+ "models.codon.MG_REV.ModelDescription":0.1035113121392619\n },\n "Node1":{\n- "models.DNA.GTR.ModelDescription":0.4820782253393885\n+ "models.codon.MG_REV.ModelDescription":0.5236339695213962\n },\n "Node12":{\n- "models.DNA.GTR.ModelDescription":0\n+ "models.codon.MG_REV.ModelDescription":0\n },\n "Node2":{\n- "models.DNA.GTR.ModelDescription":0.08259105925424247\n+ "models.codon.MG_REV.ModelDescription":0.08766202644314423\n },\n "Node3":{\n- "models.DNA.GTR.ModelDescription":0.2526911684326281\n+ "models.codon.MG_REV.ModelDescription":0.2629569437833751\n },\n "Node8":{\n- "models.DNA.GTR.ModelDescription":0.06531857233184223\n+ "models.codon.MG_REV.ModelDescription":0.07018254851044582\n },\n "Node9":{\n- "models.DNA.GTR.ModelDescription":0.03361817454867485\n+ "models.codon.MG_REV.ModelDescription":0.03334231749233734\n },\n "Pig":{\n- "models.DNA.GTR.ModelDescription":0\n+ "models.codon.MG_REV.ModelDescription":0\n },\n "Rat":{\n- "models.DNA.GTR.ModelDescription":0.0888784436278628\n+ "models.codon.MG_REV.ModelDescription":0.1018034850081214\n },\n "RhMonkey":{\n- "models.DNA.GTR.ModelDescription":0\n+ "models.codon.MG_REV.ModelDescription":0\n }\n },\n "attributes":{\n- "models.DNA.GTR.ModelDescription":{\n+ "models.codon.MG_REV.ModelDescription":{\n "attribute type":"branch length",\n "display order":0\n }\n@@ -358,32 +118,32 @@\n "data partitions":{\n "0":{\n "coverage": [\n-[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] \n+[0, 1, 2, 3, 4, 5, 6, 7, 8, 9] \n ],\n "name":"bgm.filter.default"\n }\n },\n "fits":{\n- "models.DNA.GTR.ModelDescription":{\n- "AIC-c":472.7691802214979,\n- "Log Likelihood":-210.2027719289308,\n+ "models.codon.MG_REV.ModelDescription":{\n+ "AIC-c":508.3788244913426,\n+ "Log Likelihood":-208.6011769515537,\n "Rate Distributions":null,\n "display order":0,\n- "estimated parameters":24\n+ "estimated parameters":31\n }\n },\n "input":{\n- "datatype":"nucleotide",\n- "file name":"/tmp/tmpSz4m4X/job_working_directory/000/3/working/bgm_input.fa",\n+ "datatype":"codon",\n+ "file name":"/tmp/tmp_Fhyr9/job_working_directory/000/3/working/./bgm_input.fa",\n "number of sequences":10,\n- "number of sites":30,\n+ "number of sites":10,\n "trees":{\n "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)"\n }\n },\n "settings":{\n "burn-in":10000,\n- "data-type":"nucleotide",\n+ "data-type":"codon",\n "max-parents":1,\n "min-subs":1,\n "samples":100,\n@@ -394,15 +154,15 @@\n "timers":{\n "Baseline fit":{\n "order":1,\n- "timer":0\n+ "timer":3\n },\n "Network inference":{\n "order":2,\n- "timer":1\n+ "timer":0\n },\n "Overall":{\n "order":0,\n- "timer":1\n+ "timer":3\n }\n }\n }\n\\ No newline at end of file\n' |
| b |
| diff -r b678fe748dc5 -r f8d88dcef64e test-data/busted-out1.json --- a/test-data/busted-out1.json Wed Aug 21 12:22:30 2019 -0400 +++ b/test-data/busted-out1.json Thu Feb 13 15:00:14 2020 -0500 |
| [ |
| b'@@ -1,361 +1,394 @@\n {\n- "analysis":{\n- "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted jointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. Assuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio style analysis to explore which individual sites may have been subject to selection.",\n- "version":"1.2",\n- "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",\n- "authors":"Sergei L Kosakovsky Pond",\n- "contact":"spond@temple.edu",\n- "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})"\n+ "Evidence Ratios":{\n+ "constrained": [\n+[1.766356514902524, 0.9484374805763239, 0.9571091930814299, 1.845676838710576, 1.513819401189324, 2.11256226458989, 7.366103227625151, 3.937756516229049, 2.586067836907899, 0.722379841928909, 0.3151239046214458, 1.502917468627881, 0.6499879033472316, 1.047489715978757, 1.060206108705189, 0.5038296392390414, 0.8532658611088545, 1.114374823999701, 0.5611409841208096, 0.6702870396165613, 0.4604115167079821, 0.3988433224622866, 2.47019807349414, 0.9858342091732886, 1.106653406611749, 1.067348070135177, 1.77412165088655, 1.321424873505688, 1.90457149631063, 0.7888758683589224, 0.7229203540914775, 0.8813401886687667, 0.6954297746421804, 4.613654710605887, 0.4975309466317643, 1.84565076502724, 0.6214894235132998, 0.9480915704528677, 0.9669462933548731, 1.488081789562878, 1.368539685217942, 1.726522735566884, 1.222915324989829, 0.7085094082639855, 0.3168181005885327, 2.290014391709923, 0.6343005734674315, 0.8841633809961478, 1.508078414734822, 2.666352901083321, 1.732923983135172, 3.102011384229053, 1.585109653073893, 3.345181824497555, 7.193115253213268, 3.850321954428519, 3.233128500312913, 1.977820966308441, 2.047653340750355, 0.6643430465826362, 3.624272911205855, 1.67814994913239, 1.752817561416471, 3.277248182160172, 0.3406457937754578, 0.4841828665456315, 1.399775481724447, 0.5510187898414104, 0.6276769404480749, 0.4535822272441153, 0.4226923979745105, 2.950051361271033, 0.9999999999999982, 1.027733519332009, 2.963278030618241, 2.8935730521221, 1.881916301985038, 0.4490192221083247, 3.102588216900087, 0.7028469232610687, 2.792137897266834, 0.3889955246330017, 0.9360790804326219, 0.4572233386404743, 2.908919410553763, 0.8995968442944373, 0.3261344314757346, 1.080257865601265, 1.399763176607792, 1.534646955858424, 0.4277164444783946, 2.361993404905034, 2.175584822495568, 3.122529901767528, 0.4453847841440882, 1.711825080925545, 0.8458710509917922, 2.741896592382772, 0.576439632416141, 1.142294357680513, 0.8086330800808955, 2.943414796294152, 0.833291758377592, 1.615921141634484, 0.7252129604805458, 2.833655116179036, 0.9138779988368123, 0.6174720822006171, 1.834532902825704, 0.2316812685220093, 2.479235579982967, 0.4643862206171616, 6.530720225707355, 0.4975309466317643, 1.158125132567293, 0.2987944638927862, 3.78696693228073, 0.7343025200073082, 1.93339742618843, 0.3642707474760721, 1.028034824972818, 1.511057897004292, 0.2969890376651506, 0.987605711796378, 0.3709886418939366, 4.185741574214752, 3.002372601666337, 0.424383367760914, 0.4658081554322532, 0.4024556436060775, 2.540164510486854, 0.5199349857684811, 0.4626485320487528, 0.9349816613814522, 0.5525607476128181, 0.5855612460554309, 1.85872747574379, 1.064964125964651, 3.177687923317396, 2.593304657270028, 5.234187858164534, 2.966427299030309, 1.920561682721974, 2.245869881969924, 3.811870935099101, 2.099654636695842, 3.369504334172069, 0.6379165155453101, 3.119867019567397, 0.9211859677702382, 2.195241379859611, 1.767535349740496, 1.225677095999665, 1.347676192394215, 1.671173168407676, 1.179430472478473, 1.873629958128968, 1.972321068578892, 1.863249013159319, 1.501711930393218, 2.85458165498371, 0.5332817404709185, 0.7514817421'..b'5],\n+ [0.0105618754683007],\n+ [0.0131180965046964],\n+ [0.01101098350431497],\n+ [0.0193250328267319],\n+ [0.01578738770911659],\n+ [0.0196083049972345],\n+ [0.01645869298147252],\n+ [0.01962343746171723],\n+ [0.02045785777700414],\n+ [0.008926115885166477],\n+ [0.007292098982657142],\n+ [0.009056957588961733],\n+ [0.007602170831388156],\n+ [0.007626222986467745],\n+ [0.009471947420992787],\n+ [0.007950502328516303],\n+ [0.01395367801862353],\n+ [0.01139931439306339],\n+ [0.01415821524731906],\n+ [0.01188403168729233] \n+ ],\n+ "Log Likelihood":-3467.004808147542,\n+ "Rate Distributions":{\n+ "non-synonymous/synonymous rate ratio for *test*": [\n+[0.9950576192409499, 1] \n+ ]\n+ },\n+ "display order":1,\n+ "estimated parameters":31\n+ },\n+ "Nucleotide GTR":{\n+ "AIC-c":7112.85745601076,\n+ "Equilibrium frequencies": [\n+[0.3592490842490842],\n+ [0.181959706959707],\n+ [0.240018315018315],\n+ [0.2187728937728937] \n+ ],\n+ "Log Likelihood":-3532.321297387654,\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0.5497129763145497,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.264666902964203,\n+ "Substitution rate from nucleotide C to nucleotide G":0.4916303643305098,\n+ "Substitution rate from nucleotide C to nucleotide T":1.027924764411573,\n+ "Substitution rate from nucleotide G to nucleotide T":0.304615404570875\n+ },\n+ "display order":0,\n+ "estimated parameters":24\n+ },\n+ "Unconstrained model":{\n+ "AIC-c":6910.766610587704,\n+ "Log Likelihood":-3414.486640449675,\n+ "Rate Distributions":{\n+ "Synonymous site-to-site rates":{\n+ "0":{\n+ "proportion":0.2645541257391169,\n+ "rate":0.2747941124675511\n+ },\n+ "1":{\n+ "proportion":0.6325830460054784,\n+ "rate":0.9734675888351726\n+ },\n+ "2":{\n+ "proportion":0.1028628282554047,\n+ "rate":3.028333913894314\n+ }\n+ },\n+ "Test":{\n+ "0":{\n+ "omega":0,\n+ "proportion":0.04809457608200497\n+ },\n+ "1":{\n+ "omega":0,\n+ "proportion":0.3410012743721951\n+ },\n+ "2":{\n+ "omega":1.89363684081788,\n+ "proportion":0.6109041495458\n+ }\n+ }\n+ },\n+ "display order":2,\n+ "estimated parameters":40\n+ }\n+ },\n+ "input":{\n+ "file name":"/tmp/tmp7qHfo2/job_working_directory/000/3/working/./busted_input.fa",\n+ "number of sequences":10,\n+ "number of sites":187,\n+ "partition count":1,\n+ "trees":{\n+ "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)"\n+ }\n+ },\n "test results":{\n- "LRT":44.77492170961614,\n- "p-value":1.893429857346973e-10\n+ "LRT":10.17362366082671,\n+ "p-value":0.003088842014430382\n+ },\n+ "tested":{\n+ "0":{\n+ "Baboon":"test",\n+ "Cat":"test",\n+ "Chimp":"test",\n+ "Cow":"test",\n+ "Horse":"test",\n+ "Human":"test",\n+ "Mouse":"test",\n+ "Node1":"test",\n+ "Node12":"test",\n+ "Node2":"test",\n+ "Node3":"test",\n+ "Node8":"test",\n+ "Node9":"test",\n+ "Pig":"test",\n+ "Rat":"test",\n+ "RhMonkey":"test"\n+ }\n+ },\n+ "timers":{\n+ "Constrained BUSTED model fitting":{\n+ "order":3,\n+ "timer":62\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":228\n+ },\n+ "Preliminary model fitting":{\n+ "order":1,\n+ "timer":3\n+ },\n+ "Unconstrained BUSTED model fitting":{\n+ "order":2,\n+ "timer":161\n+ }\n }\n }\n\\ No newline at end of file\n' |
| b |
| diff -r b678fe748dc5 -r f8d88dcef64e test-data/gard-out1.nex --- a/test-data/gard-out1.nex Wed Aug 21 12:22:30 2019 -0400 +++ b/test-data/gard-out1.nex Thu Feb 13 15:00:14 2020 -0500 |
| b |
| b"@@ -3,7 +3,7 @@\n BEGIN TAXA;\n \tDIMENSIONS NTAX = 21;\n \tTAXLABELS\n-\t\t'TREESPARROW_HENAN_1_2004' 'HUMAN_VIETNAM_CL105_2005' 'TREESPARROW_HENAN_4_2004' 'CHICKEN_HEBEI_326_2005' 'CHICKEN_HONGKONG_915_97' 'VIETNAM_3062_2004' 'GOOSE_HONGKONG_W355_97' 'DUCK_HONGKONG_Y283_97' 'DUCK_VIETNAM_376_2005' 'MALLARD_VIETNAM_16_2003' 'CHICKEN_THAILAND_KANCHANABURI_CK_160_2005' 'DUCK_GUANGZHOU_20_2005' 'CK_HK_WF157_2003' 'SWINE_ANHUI_2004' 'DUCK_VIETNAM_272_2005' 'HONGKONG_97_98' 'GOOSE_SHANTOU_2216_2005' 'TREESPARROW_HENAN_3_2004' 'PEREGRINEFALCON_HK_D0028_2004' 'TREESPARROW_HENAN_2_2004' 'HONGKONG_538_97' ;\n+\t\t'TREESPARROW_HENAN_1_2004' 'TREESPARROW_HENAN_3_2004' 'TREESPARROW_HENAN_4_2004' 'CHICKEN_HEBEI_326_2005' 'SWINE_ANHUI_2004' 'TREESPARROW_HENAN_2_2004' 'CHICKEN_HONGKONG_915_97' 'GOOSE_HONGKONG_W355_97' 'DUCK_HONGKONG_Y283_97' 'HONGKONG_97_98' 'HONGKONG_538_97' 'DUCK_GUANGZHOU_20_2005' 'GOOSE_SHANTOU_2216_2005' 'PEREGRINEFALCON_HK_D0028_2004' 'CK_HK_WF157_2003' 'HUMAN_VIETNAM_CL105_2005' 'DUCK_VIETNAM_376_2005' 'VIETNAM_3062_2004' 'MALLARD_VIETNAM_16_2003' 'CHICKEN_THAILAND_KANCHANABURI_CK_160_2005' 'DUCK_VIETNAM_272_2005' ;\n END;\n \n BEGIN CHARACTERS;\n@@ -16,240 +16,35 @@\n \n MATRIX\n \t'TREESPARROW_HENAN_1_2004' ATGGAGAAAATAGTGCTTCTTCGTGCAATGATCAATCTTGTTAAAAGTGATCAGATTGGCGTTGGTTACCATGCAGACTACTCGACAGAGCAGGGTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATATTGGAAAAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAATTTTGAAAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAGTGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAAAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGGGCTACAATAATACCAACCCAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCAAAGTAAATGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGACGCTATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACCAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACAGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAAGGTCCGACTACAACTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT\n-\t'HUMAN_VIETNAM_CL105_2005' ATGGAGAAAATAGTGCTTCTTTTTGCGATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTACTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGTCAATCCAGTCAATGACCTCTGTTACCCAGGGGTTTTCAATGACTATGAAGAATTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAGTCATGAAGCCTCATTAGGGGTGAGCTCAGTATGTCCATACCAGGGAAAGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTAATATGGGGGATTCATCATCCTAATGATGCGGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGGACATCAACACTAAACCAGAGATTGGTACCAAGAATAGCTACTAGATCCAAAGTAAACGGGCAAAGTGGGAGGATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAGATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAATATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCAGAAATAGCCCTCAAAAA"..b'7)Node6:0.006520820816328921,((DUCK_GUANGZHOU_20_2005:0.009483822383439561,(GOOSE_SHANTOU_2216_2005:0.007374093130581441,PEREGRINEFALCON_HK_D0028_2004:0.007242107381463219)Node14:0.0007056004954733679)Node12:0.00710363602212726,CK_HK_WF157_2003:0.00757594740908166)Node11:0.004227199989057285)Node5:0.001170889307235767,TREESPARROW_HENAN_3_2004:0.008919169512223372)Node4:0.0008380584919822353,(TREESPARROW_HENAN_4_2004:0.006708184198226799,((CHICKEN_HONGKONG_915_97:1e-10,(HONGKONG_97_98:0.006483231977175029,HONGKONG_538_97:1e-10)Node24:0.0003031375872603963)Node22:0.0001037022453470389,(GOOSE_HONGKONG_W355_97:1e-10,DUCK_HONGKONG_Y283_97:1e-10)Node27:0.002891685438446985)Node21:0.02744187404194088)Node19:0.002944759819938243)Node3:0.001672904530995233,SWINE_ANHUI_2004:0.01260983958335299)Node2:0.01303612329048956,DUCK_VIETNAM_272_2005:0.008088746451854261)Node1:0.0006545914783555439,((HUMAN_VIETNAM_CL105_2005:0.01105269263722943,DUCK_VIETNAM_376_2005:0.006417734235732284)Node33:0.002021990910251294,VIETNAM_3062_2004:0.002304874937323682)Node32:0.0006817702832121299,(MALLARD_VIETNAM_16_2003:0.005709114871229771,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.008864540916547606)Node37:9.336374870077841e-05);\n+\tTREE tree_2 = ((((((TREESPARROW_HENAN_1_2004:0.002586740118529802,TREESPARROW_HENAN_3_2004:0.003828953390398881)Node5:0.00187457851284572,TREESPARROW_HENAN_4_2004:0.0002656521581222459)Node4:0.008299727091877812,((CHICKEN_HEBEI_326_2005:0.01484958179784225,(SWINE_ANHUI_2004:1e-10,TREESPARROW_HENAN_2_2004:0.002239639293515125)Node12:0.01361271232984685)Node10:0.01278549184522065,((CHICKEN_HONGKONG_915_97:1e-10,GOOSE_HONGKONG_W355_97:1e-10)Node16:0.001326679361120118,((DUCK_HONGKONG_Y283_97:0.0006676977779578139,HONGKONG_538_97:1e-10)Node20:0.0006271503105586317,HONGKONG_97_98:0.004109899012531796)Node19:0.001653355437332724)Node15:0.01224714418221361)Node9:0.003429034672045344)Node3:0.005031763140085913,(((DUCK_GUANGZHOU_20_2005:0.004262245747717084,GOOSE_SHANTOU_2216_2005:0.004308213533754201)Node26:0.002157320455556664,CK_HK_WF157_2003:0.00647028357035998)Node25:4.000752717957338e-05,PEREGRINEFALCON_HK_D0028_2004:0.002090471815463569)Node24:0.003260422306103818)Node2:0.00707214212698231,DUCK_VIETNAM_272_2005:0.01454290899825338)Node1:0.0007147389821184919,(((HUMAN_VIETNAM_CL105_2005:0.004710041013757377,DUCK_VIETNAM_376_2005:0.01496207542884359)Node34:0.001166828623060772,MALLARD_VIETNAM_16_2003:0.003061545152147631)Node33:0.001134022328667363,VIETNAM_3062_2004:1e-10)Node32:0.0002767006572468676,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.00405819047265216);\n+\tTREE tree_3 = (TREESPARROW_HENAN_1_2004:1.793736422068138e-05,((TREESPARROW_HENAN_3_2004:0.005512611253559831,TREESPARROW_HENAN_4_2004:0.000171467489882283)Node3:0.001655366533442949,(CHICKEN_HEBEI_326_2005:0.005483900345571787,(SWINE_ANHUI_2004:0.006320038544899231,(((CHICKEN_HONGKONG_915_97:1e-10,HONGKONG_97_98:1e-10)Node12:0.001309621960005619,(GOOSE_HONGKONG_W355_97:1e-10,HONGKONG_538_97:1e-10)Node15:0.0005799496924062597)Node11:0.01406566295495963,((DUCK_HONGKONG_Y283_97:999.9836725287659,(((HUMAN_VIETNAM_CL105_2005:0.002027831968935447,DUCK_VIETNAM_376_2005:0.003754856650868615)Node23:0.00177604858958343,(VIETNAM_3062_2004:0.002068037509299944,MALLARD_VIETNAM_16_2003:1e-10)Node26:0.0001623690336813484)Node22:0.0008290773242978894,(CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.004523465945045592,DUCK_VIETNAM_272_2005:0.005056282226890766)Node29:0.001128740164377167)Node21:0.01150309854222087)Node19:0.001994389759866116,(((DUCK_GUANGZHOU_20_2005:0.003847909099661096,GOOSE_SHANTOU_2216_2005:0.005686200296849465)Node34:0.006130725555048717,PEREGRINEFALCON_HK_D0028_2004:8.387427766777967e-05)Node33:0.0009906361822363255,CK_HK_WF157_2003:0.005714641337818262)Node32:0.004952071733007253)Node18:0.002028752021615747)Node10:0.004186888950236505)Node8:0.002350770416932014)Node6:0.002154523112988181)Node2:0.0002651492563879275,TREESPARROW_HENAN_2_2004:0.007562549920247083);\n+END;\n' 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