Mercurial > repos > iuc > hyphy_bgm

annotate test-data/relax-out1.json @ 34:4515f2f64e13 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 821e0f3e4546bc55e093ab63bd9f9b57f2bf772d
author iuc
date Thu, 18 Aug 2022 14:01:09 +0000
parents 5b6b8b08f1a9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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1 {
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d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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2 "analysis":0,
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iuc
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3 "branch attributes":{
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iuc
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4 "0":{
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5 "Baboon":{
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6 "General descriptive":0.001859058366368826,
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7 "MG94xREV with separate rates for branch sets":0.001769294089885709,
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iuc
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8 "Nucleotide GTR":0.001685167654714891,
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diff changeset
9 "RELAX alternative":0.001873708670384941,
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10 "RELAX null":0.001859167714920677,
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12 "k (general descriptive)":0.09969742933359635,
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iuc
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13 "original name":"Baboon"
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bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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14 },
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15 "Cat":{
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16 "General descriptive":0.3650161006190072,
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18 "Nucleotide GTR":0.2660536011315811,
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20 "RELAX null":0.3167334440346762,
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22 "k (general descriptive)":2.319877215422834,
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23 "original name":"Cat"
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24 },
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25 "Chimp":{
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26 "General descriptive":0.001895983937468787,
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28 "Nucleotide GTR":0.001820258053351119,
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33 "original name":"Chimp"
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34 },
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35 "Cow":{
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36 "General descriptive":0.3737128696500712,
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38 "Nucleotide GTR":0.2480198736772598,
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40 "RELAX null":0.2931467439343907,
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41 "RELAX partitioned descriptive":0.3469082289876269,
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42 "k (general descriptive)":2.852150041266453,
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43 "original name":"Cow"
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44 },
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45 "Horse":{
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48 "Nucleotide GTR":0.2090998951755368,
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52 "k (general descriptive)":1.929916608813313,
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53 "original name":"Horse"
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54 },
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55 "Human":{
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58 "Nucleotide GTR":0,
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59 "RELAX alternative":0,
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60 "RELAX null":0,
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63 "original name":"Human"
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64 },
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65 "Mouse":{
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66 "General descriptive":0.1308809509233143,
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68 "Nucleotide GTR":0.1181058300538561,
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73 "original name":"Mouse"
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74 },
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75 "Node1":{
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76 "General descriptive":0.3500691487967139,
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78 "Nucleotide GTR":0.2767105173979571,
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80 "RELAX null":0.4352096867868785,
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81 "RELAX partitioned descriptive":0.4379872513902164,
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139 "Rat":{
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142 "Nucleotide GTR":0.06661490534189227,
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diff changeset
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149 "RhMonkey":{
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diff changeset
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diff changeset
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160 "attributes":{
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diff changeset
162 "attribute type":"branch length",
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diff changeset
165 "MG94xREV with separate rates for branch sets":{
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166 "attribute type":"branch length",
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167 "display order":1
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168 },
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169 "Nucleotide GTR":{
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170 "attribute type":"branch length",
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171 "display order":0
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173 "RELAX alternative":{
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174 "attribute type":"branch length",
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175 "display order":2
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177 "RELAX null":{
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178 "attribute type":"branch length",
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179 "display order":3
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180 },
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181 "RELAX partitioned descriptive":{
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182 "attribute type":"branch length",
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183 "display order":5
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184 },
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185 "k (general descriptive)":{
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186 "attribute type":"branch label",
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187 "display order":4
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189 "original name":{
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190 "attribute type":"node label",
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191 "display order":-1
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192 }
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193 }
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195 "data partitions":{
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196 "0":{
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197 "coverage": [
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199 ],
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200 "name":"relax.filter.default"
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201 }
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202 },
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203 "fits":{
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204 "General descriptive":{
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205 "AIC-c":6945.892677835464,
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diff changeset
206 "Log Likelihood":-3420.487593043145,
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207 "Rate Distributions":{
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208 "Shared":{
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209 "0":{
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210 "omega":2.201451464048879e-18,
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diff changeset
211 "proportion":0.3073650505039141
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212 },
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213 "1":{
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214 "omega":2.201451464048879e-18,
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diff changeset
215 "proportion":0.2383891488636319
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216 },
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217 "2":{
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218 "omega":2.201451281679838,
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219 "proportion":0.4542458006324541
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220 }
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221 }
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222 },
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223 "display order":4,
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diff changeset
224 "estimated parameters":51
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225 },
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226 "MG94xREV with separate rates for branch sets":{
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diff changeset
227 "AIC-c":6987.566513560764,
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228 "Equilibrium frequencies": [
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289 [0.01189287130232129]
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290 ],
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iuc
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291 "Log Likelihood":-3461.208406480981,
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292 "Rate Distributions":{
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293 "non-synonymous/synonymous rate ratio for *Reference*": [
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iuc
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294 [0.7685912547191639, 1]
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295 ],
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296 "non-synonymous/synonymous rate ratio for *Test*": [
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297 [1.603198088111489, 1]
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298 ]
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299 },
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diff changeset
300 "display order":1,
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301 "estimated parameters":32
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302 },
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diff changeset
303 "Nucleotide GTR":{
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iuc
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diff changeset
304 "AIC-c":7112.857288723968,
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305 "Equilibrium frequencies": [
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306 [0.3592490842490842],
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307 [0.181959706959707],
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309 [0.2187728937728937]
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310 ],
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iuc
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diff changeset
311 "Log Likelihood":-3532.321213744258,
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312 "Rate Distributions":{
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313 "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,
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diff changeset
314 "Substitution rate from nucleotide A to nucleotide G":1,
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iuc
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diff changeset
315 "Substitution rate from nucleotide A to nucleotide T":0.2646800222727828,
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iuc
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diff changeset
316 "Substitution rate from nucleotide C to nucleotide G":0.4918071762416347,
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iuc
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diff changeset
317 "Substitution rate from nucleotide C to nucleotide T":1.028675134787727,
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iuc
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diff changeset
318 "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741
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319 },
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320 "display order":0,
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diff changeset
321 "estimated parameters":24
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diff changeset
322 },
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diff changeset
323 "RELAX alternative":{
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iuc
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diff changeset
324 "AIC-c":6931.926773483473,
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diff changeset
325 "Log Likelihood":-3429.236709163995,
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diff changeset
326 "Rate Distributions":{
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diff changeset
327 "Reference":{
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iuc
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diff changeset
328 "0":{
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iuc
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diff changeset
329 "omega":1.761161171239182e-19,
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iuc
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diff changeset
330 "proportion":0.2691773911207853
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diff changeset
331 },
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iuc
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diff changeset
332 "1":{
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iuc
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diff changeset
333 "omega":1.762922332410267e-19,
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iuc
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diff changeset
334 "proportion":0.2692122656891806
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iuc
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diff changeset
335 },
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iuc
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336 "2":{
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iuc
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diff changeset
337 "omega":2.208286837998088,
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iuc
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diff changeset
338 "proportion":0.4616103431900341
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d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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339 }
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iuc
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diff changeset
340 },
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iuc
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341 "Test":{
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iuc
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342 "0":{
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iuc
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343 "omega":1.673670300056362e-44,
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iuc
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diff changeset
344 "proportion":0.2691773911207853
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iuc
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345 },
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iuc
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346 "1":{
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iuc
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347 "omega":1.677579612236672e-44,
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iuc
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diff changeset
348 "proportion":0.2692122656891806
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349 },
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iuc
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350 "2":{
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iuc
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diff changeset
351 "omega":6.354762788556926,
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iuc
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diff changeset
352 "proportion":0.4616103431900341
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d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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353 }
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iuc
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354 }
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iuc
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355 },
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iuc
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diff changeset
356 "display order":2,
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iuc
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diff changeset
357 "estimated parameters":36
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iuc
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358 },
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iuc
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359 "RELAX null":{
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iuc
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diff changeset
360 "AIC-c":6946.648596594286,
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iuc
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diff changeset
361 "Log Likelihood":-3437.63727539638,
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iuc
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diff changeset
362 "Rate Distributions":{
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iuc
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363 "Reference":{
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iuc
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364 "0":{
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iuc
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365 "omega":1.408928936991542e-20,
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iuc
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diff changeset
366 "proportion":0.265244047162938
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367 },
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iuc
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368 "1":{
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iuc
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diff changeset
369 "omega":1.410337865928411e-20,
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iuc
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diff changeset
370 "proportion":0.28512630848952
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iuc
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371 },
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iuc
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372 "2":{
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iuc
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diff changeset
373 "omega":3.213510017765925,
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iuc
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diff changeset
374 "proportion":0.4496296443475419
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iuc
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375 }
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iuc
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376 },
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iuc
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377 "Test":{
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iuc
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378 "0":{
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iuc
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379 "omega":1.408928936991542e-20,
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iuc
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diff changeset
380 "proportion":0.265244047162938
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iuc
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381 },
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iuc
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382 "1":{
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iuc
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diff changeset
383 "omega":1.410337865928411e-20,
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iuc
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diff changeset
384 "proportion":0.28512630848952
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385 },
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iuc
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386 "2":{
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iuc
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diff changeset
387 "omega":3.213510017765925,
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iuc
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diff changeset
388 "proportion":0.4496296443475419
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389 }
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iuc
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390 }
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iuc
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391 },
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iuc
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diff changeset
392 "display order":3,
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iuc
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diff changeset
393 "estimated parameters":35
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iuc
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394 },
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iuc
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395 "RELAX partitioned descriptive":{
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iuc
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diff changeset
396 "AIC-c":6937.049237937651,
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iuc
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diff changeset
397 "Log Likelihood":-3427.627954124649,
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iuc
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diff changeset
398 "Rate Distributions":{
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iuc
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399 "Reference":{
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iuc
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400 "0":{
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iuc
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diff changeset
401 "omega":0.1847557016619168,
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iuc
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diff changeset
402 "proportion":0.4766160247339328
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403 },
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iuc
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404 "1":{
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iuc
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diff changeset
405 "omega":0.3367540359539261,
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iuc
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diff changeset
406 "proportion":0.3005513276312735
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407 },
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iuc
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408 "2":{
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iuc
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diff changeset
409 "omega":4.272816072857538,
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iuc
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diff changeset
410 "proportion":0.2228326476347937
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411 }
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iuc
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412 },
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iuc
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diff changeset
413 "Test":{
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iuc
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414 "0":{
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iuc
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diff changeset
415 "omega":1.127143149593234e-21,
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iuc
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diff changeset
416 "proportion":0.2367540589657237
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417 },
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iuc
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418 "1":{
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iuc
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diff changeset
419 "omega":1.128270292740756e-21,
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iuc
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diff changeset
420 "proportion":0.2771164325302933
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421 },
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iuc
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diff changeset
422 "2":{
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5b6b8b08f1a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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diff changeset
423 "omega":6.023626417874829,
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iuc
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diff changeset
424 "proportion":0.4861295085039831
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d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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425 }
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426 }
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427 },
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diff changeset
428 "display order":5,
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diff changeset
429 "estimated parameters":40
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430 }
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diff changeset
431 },
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diff changeset
432 "input":{
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5b6b8b08f1a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
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diff changeset
433 "file name":"/tmp/tmpkgsdjj1d/job_working_directory/000/3/working/./input.fasta",
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d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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diff changeset
434 "number of sequences":10,
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diff changeset
435 "number of sites":187,
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diff changeset
436 "partition count":1,
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diff changeset
437 "trees":{
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iuc
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diff changeset
438 "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)"
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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439 }
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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diff changeset
440 },
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5b6b8b08f1a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents: 25
diff changeset
441 "runtime":"2.5.32",
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d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
442 "test results":{
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5b6b8b08f1a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
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diff changeset
443 "LRT":16.80113246476958,
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iuc
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diff changeset
444 "p-value":4.150852429507523e-05,
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iuc
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diff changeset
445 "relaxation or intensification parameter":2.334214628944839
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d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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diff changeset
446 },
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iuc
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diff changeset
447 "tested":{
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iuc
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diff changeset
448 "0":{
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iuc
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diff changeset
449 "Baboon":"Reference",
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
450 "Cat":"Test",
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
451 "Chimp":"Reference",
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
452 "Cow":"Test",
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
453 "Horse":"Test",
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
454 "Human":"Reference",
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
455 "Mouse":"Reference",
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
456 "Node1":"Reference",
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
457 "Node12":"Reference",
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
458 "Node2":"Reference",
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
459 "Node3":"Reference",
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
460 "Node8":"Reference",
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iuc
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diff changeset
461 "Node9":"Reference",
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iuc
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diff changeset
462 "Pig":"Reference",
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
463 "Rat":"Reference",
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
464 "RhMonkey":"Reference"
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
465 }
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
466 },
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iuc
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diff changeset
467 "timers":{
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iuc
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diff changeset
468 "General descriptive model fitting":{
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diff changeset
469 "order":2,
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5b6b8b08f1a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
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diff changeset
470 "timer":127
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d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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diff changeset
471 },
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iuc
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diff changeset
472 "Overall":{
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diff changeset
473 "order":0,
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5b6b8b08f1a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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diff changeset
474 "timer":396
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diff changeset
475 },
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diff changeset
476 "Preliminary model fitting":{
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diff changeset
477 "order":1,
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diff changeset
478 "timer":8
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diff changeset
479 },
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diff changeset
480 "RELAX alternative model fitting":{
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diff changeset
481 "order":3,
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5b6b8b08f1a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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diff changeset
482 "timer":103
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diff changeset
483 },
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diff changeset
484 "RELAX null model fitting":{
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diff changeset
485 "order":4,
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5b6b8b08f1a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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diff changeset
486 "timer":41
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d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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diff changeset
487 },
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diff changeset
488 "RELAX partitioned descriptive":{
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489 "order":5,
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5b6b8b08f1a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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490 "timer":116
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d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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491 }
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492 }
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493 }