| Previous changeset 1:0f108ee932ea (2019-08-21) Next changeset 3:b73b35db4664 (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_fubar.xml macros.xml test-data/bgm-out1.json test-data/busted-out1.json test-data/gard-out1.nex |
| b |
| diff -r 0f108ee932ea -r 6943fbec145c hyphy_fubar.xml --- a/hyphy_fubar.xml Wed Aug 21 12:24:34 2019 -0400 +++ b/hyphy_fubar.xml Thu Feb 13 15:01:46 2020 -0500 |
| b |
| @@ -52,6 +52,10 @@ Model-based selection analyses (such as those performed by PAML and HyPhy) can be slow, becoming impractical for large alignments. We present a method to model and detect selection much faster than existing methods and to leverage Bayesian MCMC to robustly account for parameter estimation errors. Results: By exploiting some commonly used approximations, FUBAR can perform detection of positive selection under a model that allows rich site- to-site rate variation about 30 to 50 times faster than existing random effects likelihood methods, and 10 to 30 times faster than existing fixed effects likelihood methods. We introduce an ultra-fast MCMC routine that allows a flexible prior specification, with no parametric constraints on the prior shape. Furthermore, our method allows us to visualize Bayesian inference for each site, revealing the model supported by the data. + +See the online documentation_ for more information. + +.. _documentation: http://hyphy.org/methods/selection-methods/#fubar ]]></help> <expand macro="citations"> <citation type="doi">10.1093/molbev/mst030</citation> |
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| diff -r 0f108ee932ea -r 6943fbec145c macros.xml --- a/macros.xml Wed Aug 21 12:24:34 2019 -0400 +++ b/macros.xml Thu Feb 13 15:01:46 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 0f108ee932ea -r 6943fbec145c test-data/bgm-out1.json --- a/test-data/bgm-out1.json Wed Aug 21 12:24:34 2019 -0400 +++ b/test-data/bgm-out1.json Thu Feb 13 15:01:46 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 0f108ee932ea -r 6943fbec145c test-data/busted-out1.json --- a/test-data/busted-out1.json Wed Aug 21 12:24:34 2019 -0400 +++ b/test-data/busted-out1.json Thu Feb 13 15:01:46 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 0f108ee932ea -r 6943fbec145c test-data/gard-out1.nex --- a/test-data/gard-out1.nex Wed Aug 21 12:24:34 2019 -0400 +++ b/test-data/gard-out1.nex Thu Feb 13 15:01:46 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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