Mercurial > repos > iuc > hyphy_relax

annotate test-data/relax-out1.json @ 33:7207313de5a8 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 13:59:18 +0000
parents 49885a825dc1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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551616a65f8f "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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2 "analysis":0,
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3 "branch attributes":{
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4 "0":{
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5 "Baboon":{
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14 },
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
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diff changeset
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diff changeset
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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diff changeset
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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102 "Node3":{
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iuc
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diff changeset
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diff changeset
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diff changeset
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iuc
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
parents:
diff changeset
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iuc
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diff changeset
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diff changeset
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iuc
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diff changeset
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iuc
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iuc
parents:
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iuc
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120 "Node9":{
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diff changeset
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iuc
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diff changeset
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diff changeset
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diff changeset
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iuc
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diff changeset
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iuc
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iuc
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129 "Pig":{
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diff changeset
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
parents: 25
diff changeset
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iuc
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diff changeset
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iuc
parents: 0
diff changeset
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iuc
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diff changeset
139 "Rat":{
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iuc
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diff changeset
140 "General descriptive":0.07157977734335202,
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parents: 25
diff changeset
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iuc
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diff changeset
142 "Nucleotide GTR":0.06661490534189227,
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
parents: 25
diff changeset
145 "RELAX partitioned descriptive":0.0757525093290258,
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iuc
parents: 25
diff changeset
146 "k (general descriptive)":1.316568267879453,
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iuc
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diff changeset
147 "original name":"Rat"
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iuc
parents: 0
diff changeset
148 },
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iuc
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diff changeset
149 "RhMonkey":{
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iuc
parents: 25
diff changeset
150 "General descriptive":0.003672848089716511,
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diff changeset
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iuc
parents: 25
diff changeset
152 "Nucleotide GTR":0.003778804730491441,
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iuc
parents: 25
diff changeset
153 "RELAX alternative":0.003633278464154418,
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iuc
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diff changeset
154 "RELAX null":0.003661271320845124,
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iuc
parents: 25
diff changeset
155 "RELAX partitioned descriptive":0.003625957794514879,
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iuc
parents: 25
diff changeset
156 "k (general descriptive)":5.196295069596697,
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iuc
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diff changeset
157 "original name":"RhMonkey"
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iuc
parents:
diff changeset
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parents:
diff changeset
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iuc
parents:
diff changeset
160 "attributes":{
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161 "General descriptive":{
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parents:
diff changeset
162 "attribute type":"branch length",
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diff changeset
163 "display order":4
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diff changeset
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iuc
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diff changeset
166 "attribute type":"branch length",
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diff changeset
167 "display order":1
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diff changeset
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diff changeset
169 "Nucleotide GTR":{
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iuc
parents:
diff changeset
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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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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185 "k (general descriptive)":{
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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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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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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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diff changeset
211 "proportion":0.3073650505039141
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213 "1":{
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215 "proportion":0.2383891488636319
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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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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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290 ],
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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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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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297 [1.603198088111489, 1]
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298 ]
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299 },
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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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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
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diff changeset
304 "AIC-c":7112.857288723968,
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305 "Equilibrium frequencies": [
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309 [0.2187728937728937]
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310 ],
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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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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
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diff changeset
315 "Substitution rate from nucleotide A to nucleotide T":0.2646800222727828,
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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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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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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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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diff changeset
328 "0":{
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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diff changeset
329 "omega":1.761161171239182e-19,
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diff changeset
330 "proportion":0.2691773911207853
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diff changeset
331 },
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diff changeset
332 "1":{
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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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diff changeset
335 },
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diff changeset
336 "2":{
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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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diff changeset
339 }
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diff changeset
340 },
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iuc
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diff changeset
341 "Test":{
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diff changeset
342 "0":{
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
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diff changeset
343 "omega":1.673670300056362e-44,
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diff changeset
344 "proportion":0.2691773911207853
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345 },
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iuc
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346 "1":{
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
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diff changeset
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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353 }
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iuc
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diff changeset
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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diff changeset
359 "RELAX null":{
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
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diff changeset
360 "AIC-c":6946.648596594286,
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iuc
parents: 25
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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diff changeset
364 "0":{
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iuc
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diff changeset
365 "omega":1.408928936991542e-20,
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iuc
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diff changeset
366 "proportion":0.265244047162938
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iuc
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367 },
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iuc
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368 "1":{
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
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diff changeset
369 "omega":1.410337865928411e-20,
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iuc
parents: 25
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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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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diff changeset
379 "omega":1.408928936991542e-20,
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iuc
parents: 25
diff changeset
380 "proportion":0.265244047162938
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iuc
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diff changeset
381 },
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iuc
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diff changeset
382 "1":{
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iuc
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diff changeset
383 "omega":1.410337865928411e-20,
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iuc
parents: 25
diff changeset
384 "proportion":0.28512630848952
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iuc
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385 },
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iuc
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diff changeset
386 "2":{
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iuc
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diff changeset
387 "omega":3.213510017765925,
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iuc
parents: 25
diff changeset
388 "proportion":0.4496296443475419
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iuc
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diff changeset
389 }
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iuc
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diff changeset
390 }
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iuc
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diff changeset
391 },
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iuc
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diff changeset
392 "display order":3,
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iuc
parents: 0
diff changeset
393 "estimated parameters":35
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iuc
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diff changeset
394 },
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iuc
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diff changeset
395 "RELAX partitioned descriptive":{
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents: 25
diff changeset
396 "AIC-c":6937.049237937651,
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iuc
parents: 25
diff changeset
397 "Log Likelihood":-3427.627954124649,
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iuc
parents: 0
diff changeset
398 "Rate Distributions":{
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iuc
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diff changeset
399 "Reference":{
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iuc
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diff changeset
400 "0":{
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iuc
parents: 25
diff changeset
401 "omega":0.1847557016619168,
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iuc
parents: 25
diff changeset
402 "proportion":0.4766160247339328
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iuc
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diff changeset
403 },
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iuc
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diff changeset
404 "1":{
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents: 25
diff changeset
405 "omega":0.3367540359539261,
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iuc
parents: 25
diff changeset
406 "proportion":0.3005513276312735
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iuc
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diff changeset
407 },
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iuc
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diff changeset
408 "2":{
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents: 25
diff changeset
409 "omega":4.272816072857538,
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iuc
parents: 25
diff changeset
410 "proportion":0.2228326476347937
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diff changeset
411 }
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iuc
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diff changeset
412 },
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iuc
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diff changeset
413 "Test":{
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iuc
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diff changeset
414 "0":{
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents: 25
diff changeset
415 "omega":1.127143149593234e-21,
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iuc
parents: 25
diff changeset
416 "proportion":0.2367540589657237
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iuc
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diff changeset
417 },
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iuc
parents: 0
diff changeset
418 "1":{
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iuc
parents: 25
diff changeset
419 "omega":1.128270292740756e-21,
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iuc
parents: 25
diff changeset
420 "proportion":0.2771164325302933
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iuc
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diff changeset
421 },
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iuc
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diff changeset
422 "2":{
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iuc
parents: 25
diff changeset
423 "omega":6.023626417874829,
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iuc
parents: 25
diff changeset
424 "proportion":0.4861295085039831
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a4c5dc437558 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
425 }
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iuc
parents: 0
diff changeset
426 }
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iuc
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diff changeset
427 },
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iuc
parents: 0
diff changeset
428 "display order":5,
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iuc
parents: 0
diff changeset
429 "estimated parameters":40
a4c5dc437558 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
430 }
a4c5dc437558 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
431 },
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diff changeset
432 "input":{
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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diff changeset
433 "file name":"/tmp/tmpkgsdjj1d/job_working_directory/000/3/working/./input.fasta",
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a4c5dc437558 "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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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)"
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439 }
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diff changeset
440 },
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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diff changeset
441 "runtime":"2.5.32",
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a4c5dc437558 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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diff changeset
442 "test results":{
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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diff changeset
443 "LRT":16.80113246476958,
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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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a4c5dc437558 "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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diff changeset
447 "tested":{
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diff changeset
448 "0":{
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diff changeset
449 "Baboon":"Reference",
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diff changeset
450 "Cat":"Test",
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iuc
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diff changeset
451 "Chimp":"Reference",
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iuc
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diff changeset
452 "Cow":"Test",
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diff changeset
453 "Horse":"Test",
a4c5dc437558 "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",
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iuc
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diff changeset
455 "Mouse":"Reference",
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iuc
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diff changeset
456 "Node1":"Reference",
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diff changeset
457 "Node12":"Reference",
a4c5dc437558 "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",
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iuc
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diff changeset
459 "Node3":"Reference",
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diff changeset
460 "Node8":"Reference",
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diff changeset
461 "Node9":"Reference",
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iuc
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diff changeset
462 "Pig":"Reference",
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iuc
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463 "Rat":"Reference",
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iuc
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diff changeset
464 "RhMonkey":"Reference"
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465 }
a4c5dc437558 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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diff changeset
466 },
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diff changeset
467 "timers":{
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diff changeset
468 "General descriptive model fitting":{
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diff changeset
469 "order":2,
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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470 "timer":127
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a4c5dc437558 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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471 },
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diff changeset
472 "Overall":{
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diff changeset
473 "order":0,
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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474 "timer":396
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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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479 },
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480 "RELAX alternative model fitting":{
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481 "order":3,
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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482 "timer":103
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483 },
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diff changeset
484 "RELAX null model fitting":{
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485 "order":4,
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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486 "timer":41
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487 },
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diff changeset
488 "RELAX partitioned descriptive":{
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489 "order":5,
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49885a825dc1 "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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491 }
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492 }
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493 }