| Previous changeset 0:6164d9298db9 (2019-08-21) Next changeset 2:f65e8fe7d5b8 (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_fade.xml macros.xml test-data/bgm-out1.json test-data/busted-out1.json test-data/gard-out1.nex |
| b |
| diff -r 6164d9298db9 -r da4192d32e10 hyphy_fade.xml --- a/hyphy_fade.xml Wed Aug 21 12:25:26 2019 -0400 +++ b/hyphy_fade.xml Thu Feb 13 15:02:39 2020 -0500 |
| [ |
| @@ -60,6 +60,10 @@ </tests> <help><![CDATA[ FADE (FUBAR Approach to Directional Evolution) uses the same underlying algorithmic advances as impletented in FUBAR to apply Baysian MCMC accounting of parameter uncertiantiy to detect sites evolving under directional evolution in protien alignments. + +See the online documentation_ for more information. + +.. _documentation: http://hyphy.org/methods/selection-methods/#fade ]]></help> <expand macro="citations"> <citation type="doi">10.1093/molbev/msv022</citation> |
| b |
| diff -r 6164d9298db9 -r da4192d32e10 macros.xml --- a/macros.xml Wed Aug 21 12:25:26 2019 -0400 +++ b/macros.xml Thu Feb 13 15:02:39 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 6164d9298db9 -r da4192d32e10 test-data/bgm-out1.json --- a/test-data/bgm-out1.json Wed Aug 21 12:25:26 2019 -0400 +++ b/test-data/bgm-out1.json Thu Feb 13 15:02:39 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 6164d9298db9 -r da4192d32e10 test-data/busted-out1.json --- a/test-data/busted-out1.json Wed Aug 21 12:25:26 2019 -0400 +++ b/test-data/busted-out1.json Thu Feb 13 15:02:39 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 6164d9298db9 -r da4192d32e10 test-data/gard-out1.nex --- a/test-data/gard-out1.nex Wed Aug 21 12:25:26 2019 -0400 +++ b/test-data/gard-out1.nex Thu Feb 13 15:02:39 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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