Mercurial > repos > iuc > hyphy_summary

annotate test-data/summary/nsp8.PRIME.json @ 0:f304c108aa1f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
author iuc
date Wed, 09 Jun 2021 07:03:54 +0000
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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diff changeset
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diff changeset
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diff changeset
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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diff changeset
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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diff changeset
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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iuc
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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diff changeset
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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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diff changeset
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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diff changeset
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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diff changeset
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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diff changeset
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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diff changeset
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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diff changeset
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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diff changeset
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diff changeset
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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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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diff changeset
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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iuc
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iuc
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iuc
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iuc
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diff changeset
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diff changeset
203 ]
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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204 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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205 "headers": [
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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206 ["alpha;", "Synonymous substitution rate at a site"],
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207 ["β", "Log of property independent non-synonymous rate a site"],
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208 ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"],
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209 ["PRIME LogL", "Site Log-likelihood under the PRIME model"],
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210 ["FEL LogL", "Site Log-likelihood under the FEL model"],
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211 ["p-value", "Omnibus p-value (any property is important)"],
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212 ["λ1", "Importance for Factor I bipolar"],
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
213 ["p1", "p-value for non-zero effect of Factor I bipolar"],
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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214 ["LogL1", "Log likelihood when there is no effect of Factor I bipolar"],
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parents:
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215 ["λ2", "Importance for Factor II secondary structure"],
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
216 ["p2", "p-value for non-zero effect of Factor II secondary structure"],
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
217 ["LogL2", "Log likelihood when there is no effect of Factor II secondary structure"],
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
218 ["λ3", "Importance for Factor III volume"],
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
219 ["p3", "p-value for non-zero effect of Factor III volume"],
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
220 ["LogL3", "Log likelihood when there is no effect of Factor III volume"],
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
221 ["λ4", "Importance for Factor IV composition"],
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
222 ["p4", "p-value for non-zero effect of Factor IV composition"],
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
223 ["LogL4", "Log likelihood when there is no effect of Factor IV composition"],
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
224 ["λ5", "Importance for Factor V charge"],
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
225 ["p5", "p-value for non-zero effect of Factor V charge"],
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
226 ["LogL5", "Log likelihood when there is no effect of Factor V charge"]
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
227 ]
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
228 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
229 "analysis":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
230 "authors":"Sergei L. Kosakovsky Pond",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
231 "citation":"TBD",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
232 "contact":"spond@temple.edu",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
233 "info":"PRIME (PRoperty Informed Model of Evolution). Given a set of N amino-acid properties,\n fit a site-level model where non-synonymous rates depend on how much a non-synonymous substitution changes the \n properties of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )- lambda_2 * diff_2 (X,Y) -...).\n When lambda_k > 0, changes in property k are disfavored and when lambda_k < 0 -- they are promoted.\n At each site, N tests are performed\n A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
234 "requirements":"in-frame codon alignment and a phylogenetic tree",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
235 "version":"0.0.1"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
236 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
237 "branch attributes":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
238 "0":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
239 "Node20":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
240 "Global MG94xREV":0.001634412628363601,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
241 "Nucleotide GTR":0.001684521619549293
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
242 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
243 "Node38":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
244 "Global MG94xREV":0.001735516181127408,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
245 "Nucleotide GTR":0.00168484920326581
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
246 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
247 "Node4":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
248 "Global MG94xREV":0.001634082125054255,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
249 "Nucleotide GTR":0.001683801387489096
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
250 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
251 "REFERENCE":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
252 "Global MG94xREV":0,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
253 "Nucleotide GTR":0,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
254 "original name":"REFERENCE"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
255 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
256 "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
257 "Global MG94xREV":0,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
258 "Nucleotide GTR":0,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
259 "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
260 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
261 "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
262 "Global MG94xREV":0.001732287226413535,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
263 "Nucleotide GTR":0.001682745450340891,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
264 "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
265 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
266 "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
267 "Global MG94xREV":0,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
268 "Nucleotide GTR":0,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
269 "original name":"epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
270 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
271 "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
272 "Global MG94xREV":0.001731614558297581,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
273 "Nucleotide GTR":0.00168274558227101,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
274 "original name":"epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
275 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
276 "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
277 "Global MG94xREV":0.001735723689760284,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
278 "Nucleotide GTR":0.001684401404203384,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
279 "original name":"epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
280 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
281 "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
282 "Global MG94xREV":0.001732400224923104,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
283 "Nucleotide GTR":0.00168406792173386,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
284 "original name":"epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
285 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
286 "epi_isl_1543980_hCoV_19_Singapore_490_2021":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
287 "Global MG94xREV":0.001734572372218793,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
288 "Nucleotide GTR":0.001684975469042935,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
289 "original name":"epi_isl_1543980/hCoV-19/Singapore/490/2021"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
290 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
291 "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
292 "Global MG94xREV":0.001735567212797747,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
293 "Nucleotide GTR":0.001684401583391051,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
294 "original name":"epi_isl_1544068/hCoV-19/India/MH-NCCS-RT231527/2021"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
295 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
296 "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
297 "Global MG94xREV":0.001732287290600434,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
298 "Nucleotide GTR":0.001682745512695379,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
299 "original name":"epi_isl_1573247/hCoV-19/Germany/un-RKI-I-068985/2021"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
300 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
301 "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":{
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iuc
parents:
diff changeset
302 "Global MG94xREV":0,
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iuc
parents:
diff changeset
303 "Nucleotide GTR":0,
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iuc
parents:
diff changeset
304 "original name":"epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021"
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iuc
parents:
diff changeset
305 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
306 "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":{
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iuc
parents:
diff changeset
307 "Global MG94xREV":0.001733756929863212,
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iuc
parents:
diff changeset
308 "Nucleotide GTR":0.001684431017860219,
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iuc
parents:
diff changeset
309 "original name":"epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021"
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iuc
parents:
diff changeset
310 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
311 "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":{
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iuc
parents:
diff changeset
312 "Global MG94xREV":0.001733765372843661,
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iuc
parents:
diff changeset
313 "Nucleotide GTR":0.001684439221071522,
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iuc
parents:
diff changeset
314 "original name":"epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021"
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iuc
parents:
diff changeset
315 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
316 "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":{
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iuc
parents:
diff changeset
317 "Global MG94xREV":0,
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iuc
parents:
diff changeset
318 "Nucleotide GTR":0,
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iuc
parents:
diff changeset
319 "original name":"epi_isl_1615709/hCoV-19/England/CAMC-14E792B/2021"
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iuc
parents:
diff changeset
320 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
321 "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":{
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iuc
parents:
diff changeset
322 "Global MG94xREV":0.001736016199323374,
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iuc
parents:
diff changeset
323 "Nucleotide GTR":0.00168443927661716,
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iuc
parents:
diff changeset
324 "original name":"epi_isl_1632256/hCoV-19/England/RAND-14E1D70/2021"
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iuc
parents:
diff changeset
325 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
326 "epi_isl_1652105_hCoV_19_Singapore_561_2021":{
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iuc
parents:
diff changeset
327 "Global MG94xREV":0.001733699172098583,
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iuc
parents:
diff changeset
328 "Nucleotide GTR":0.001685171120971631,
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iuc
parents:
diff changeset
329 "original name":"epi_isl_1652105/hCoV-19/Singapore/561/2021"
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iuc
parents:
diff changeset
330 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
331 "epi_isl_1652118_hCoV_19_Singapore_575_2021":{
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iuc
parents:
diff changeset
332 "Global MG94xREV":0.001733317353440973,
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iuc
parents:
diff changeset
333 "Nucleotide GTR":0.001684401899924961,
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iuc
parents:
diff changeset
334 "original name":"epi_isl_1652118/hCoV-19/Singapore/575/2021"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
335 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
336 "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":{
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iuc
parents:
diff changeset
337 "Global MG94xREV":0.01050948249155059,
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iuc
parents:
diff changeset
338 "Nucleotide GTR":0.01020457779555702,
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iuc
parents:
diff changeset
339 "original name":"gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human"
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iuc
parents:
diff changeset
340 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
341 "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":{
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iuc
parents:
diff changeset
342 "Global MG94xREV":0.02683667579915389,
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iuc
parents:
diff changeset
343 "Nucleotide GTR":0.02592331511084145,
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iuc
parents:
diff changeset
344 "original name":"gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human"
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iuc
parents:
diff changeset
345 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
346 "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":{
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iuc
parents:
diff changeset
347 "Global MG94xREV":0.005257318382497578,
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iuc
parents:
diff changeset
348 "Nucleotide GTR":0.005093980037543817,
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iuc
parents:
diff changeset
349 "original name":"gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human"
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iuc
parents:
diff changeset
350 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
351 "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":{
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iuc
parents:
diff changeset
352 "Global MG94xREV":0.003479916215882181,
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iuc
parents:
diff changeset
353 "Nucleotide GTR":0.003379296026417724,
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iuc
parents:
diff changeset
354 "original name":"gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
355 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
356 "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":{
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iuc
parents:
diff changeset
357 "Global MG94xREV":0.003464849064677958,
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iuc
parents:
diff changeset
358 "Nucleotide GTR":0.003372774424630234,
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iuc
parents:
diff changeset
359 "original name":"gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human"
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iuc
parents:
diff changeset
360 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
361 "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":{
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iuc
parents:
diff changeset
362 "Global MG94xREV":0.00347332934630856,
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iuc
parents:
diff changeset
363 "Nucleotide GTR":0.003374190595560375,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
364 "original name":"gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
365 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
366 "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":{
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iuc
parents:
diff changeset
367 "Global MG94xREV":0.00521423750425419,
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iuc
parents:
diff changeset
368 "Nucleotide GTR":0.00505933790460295,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
369 "original name":"gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
370 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
371 "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":{
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iuc
parents:
diff changeset
372 "Global MG94xREV":0.003464011560303172,
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iuc
parents:
diff changeset
373 "Nucleotide GTR":0.003373764235314068,
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iuc
parents:
diff changeset
374 "original name":"gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
375 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
376 "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":{
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iuc
parents:
diff changeset
377 "Global MG94xREV":0.005236219925335357,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
378 "Nucleotide GTR":0.005068409188375663,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
379 "original name":"gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human"
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iuc
parents:
diff changeset
380 },
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iuc
parents:
diff changeset
381 "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":{
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iuc
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diff changeset
382 "Global MG94xREV":0.003464842721718857,
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iuc
parents:
diff changeset
383 "Nucleotide GTR":0.003372774424770855,
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iuc
parents:
diff changeset
384 "original name":"gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human"
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iuc
parents:
diff changeset
385 },
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iuc
parents:
diff changeset
386 "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":{
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iuc
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diff changeset
387 "Global MG94xREV":0.001735902729272567,
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iuc
parents:
diff changeset
388 "Nucleotide GTR":0.001686266012390882,
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iuc
parents:
diff changeset
389 "original name":"gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human"
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iuc
parents:
diff changeset
390 },
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iuc
parents:
diff changeset
391 "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":{
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iuc
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diff changeset
392 "Global MG94xREV":0.003480097445990996,
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iuc
parents:
diff changeset
393 "Nucleotide GTR":0.003374436490976879,
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iuc
parents:
diff changeset
394 "original name":"gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human"
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iuc
parents:
diff changeset
395 },
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iuc
parents:
diff changeset
396 "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":{
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iuc
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diff changeset
397 "Global MG94xREV":0.003472571047451632,
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iuc
parents:
diff changeset
398 "Nucleotide GTR":0.003376034743011948,
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iuc
parents:
diff changeset
399 "original name":"gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human"
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iuc
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diff changeset
400 },
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iuc
parents:
diff changeset
401 "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":{
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iuc
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diff changeset
402 "Global MG94xREV":0.003474988463696198,
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iuc
parents:
diff changeset
403 "Nucleotide GTR":0.003374190741831846,
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iuc
parents:
diff changeset
404 "original name":"gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human"
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iuc
parents:
diff changeset
405 },
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iuc
parents:
diff changeset
406 "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":{
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iuc
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diff changeset
407 "Global MG94xREV":0.003471294880575992,
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iuc
parents:
diff changeset
408 "Nucleotide GTR":0.003376937492543959,
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iuc
parents:
diff changeset
409 "original name":"gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human"
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iuc
parents:
diff changeset
410 }
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
411 },
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iuc
parents:
diff changeset
412 "attributes":{
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iuc
parents:
diff changeset
413 "Global MG94xREV":{
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iuc
parents:
diff changeset
414 "attribute type":"branch length",
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iuc
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diff changeset
415 "display order":1
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iuc
parents:
diff changeset
416 },
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iuc
parents:
diff changeset
417 "Nucleotide GTR":{
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iuc
parents:
diff changeset
418 "attribute type":"branch length",
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iuc
parents:
diff changeset
419 "display order":0
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diff changeset
420 },
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iuc
parents:
diff changeset
421 "original name":{
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iuc
parents:
diff changeset
422 "attribute type":"node label",
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iuc
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diff changeset
423 "display order":-1
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iuc
parents:
diff changeset
424 }
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iuc
parents:
diff changeset
425 }
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iuc
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diff changeset
426 },
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iuc
parents:
diff changeset
427 "data partitions":{
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iuc
parents:
diff changeset
428 "0":{
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iuc
parents:
diff changeset
429 "coverage": [
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iuc
parents:
diff changeset
430 [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, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197]
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iuc
parents:
diff changeset
431 ],
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iuc
parents:
diff changeset
432 "name":"prime.filter.default"
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iuc
parents:
diff changeset
433 }
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diff changeset
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diff changeset
435 "fits":{
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iuc
parents:
diff changeset
436 "Global MG94xREV":{
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parents:
diff changeset
437 "AIC-c":2512.962001128159,
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iuc
parents:
diff changeset
438 "Equilibrium frequencies": [
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diff changeset
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iuc
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499 [0.02371882618448924]
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500 ],
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iuc
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diff changeset
501 "Log Likelihood":-1205.058976375664,
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diff changeset
502 "Rate Distributions":{
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diff changeset
503 "non-synonymous/synonymous rate ratio for *background*": [
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diff changeset
504 [0.4929148115989916, 1]
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505 ],
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iuc
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diff changeset
506 "non-synonymous/synonymous rate ratio for *test*": [
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diff changeset
507 [24.3195468932995, 1]
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diff changeset
508 ]
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509 },
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diff changeset
510 "display order":1,
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diff changeset
511 "estimated parameters":51
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512 },
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diff changeset
513 "Nucleotide GTR":{
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diff changeset
514 "AIC-c":2633.0046471406,
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diff changeset
515 "Equilibrium frequencies": [
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519 [0.2922979797979798]
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520 ],
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diff changeset
521 "Log Likelihood":-1247.247280799152,
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diff changeset
522 "Rate Distributions":{
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diff changeset
523 "Substitution rate from nucleotide A to nucleotide C":0,
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iuc
parents:
diff changeset
524 "Substitution rate from nucleotide A to nucleotide G":1,
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iuc
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diff changeset
525 "Substitution rate from nucleotide A to nucleotide T":0.3101631549852981,
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iuc
parents:
diff changeset
526 "Substitution rate from nucleotide C to nucleotide G":1.129990583516242,
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parents:
diff changeset
527 "Substitution rate from nucleotide C to nucleotide T":2.723444388603395,
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diff changeset
528 "Substitution rate from nucleotide G to nucleotide T":1.720896006888861
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529 },
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diff changeset
530 "display order":0,
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diff changeset
531 "estimated parameters":69
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diff changeset
532 }
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diff changeset
533 },
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diff changeset
534 "input":{
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diff changeset
535 "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas",
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iuc
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diff changeset
536 "number of sequences":32,
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diff changeset
537 "number of sites":198,
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iuc
parents:
diff changeset
538 "partition count":1,
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iuc
parents:
diff changeset
539 "trees":{
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diff changeset
540 "0":"(REFERENCE,(gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human,epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021)Node20,gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human,epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021,(epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021,gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human)Node4,epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021,gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human,gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human,epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021,gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human,(gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human,gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human,epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021)Node38,epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021,gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human,epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021,gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human,epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021,epi_isl_1543980_hCoV_19_Singapore_490_2021,epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021,gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human,epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021,gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human,gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human,epi_isl_1652118_hCoV_19_Singapore_575_2021,epi_isl_1652105_hCoV_19_Singapore_561_2021,gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human,gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human,epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
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iuc
parents:
diff changeset
542 },
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diff changeset
543 "tested":{
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diff changeset
544 "0":{
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diff changeset
545 "Node20":"test",
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iuc
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diff changeset
546 "Node38":"background",
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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
549 "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"background",
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iuc
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diff changeset
550 "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"background",
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diff changeset
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iuc
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diff changeset
552 "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"background",
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iuc
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diff changeset
553 "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"background",
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iuc
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diff changeset
554 "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"background",
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iuc
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diff changeset
555 "epi_isl_1543980_hCoV_19_Singapore_490_2021":"background",
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iuc
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diff changeset
556 "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"background",
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iuc
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diff changeset
557 "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"background",
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iuc
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diff changeset
558 "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"background",
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iuc
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diff changeset
559 "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"background",
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iuc
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diff changeset
560 "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"background",
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iuc
parents:
diff changeset
561 "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"background",
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iuc
parents:
diff changeset
562 "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"background",
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iuc
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diff changeset
563 "epi_isl_1652105_hCoV_19_Singapore_561_2021":"background",
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iuc
parents:
diff changeset
564 "epi_isl_1652118_hCoV_19_Singapore_575_2021":"background",
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iuc
parents:
diff changeset
565 "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"background",
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iuc
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diff changeset
566 "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"background",
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iuc
parents:
diff changeset
567 "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"background",
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iuc
parents:
diff changeset
568 "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"background",
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iuc
parents:
diff changeset
569 "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"background",
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iuc
parents:
diff changeset
570 "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"background",
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iuc
parents:
diff changeset
571 "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"background",
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iuc
parents:
diff changeset
572 "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":"background",
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iuc
parents:
diff changeset
573 "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":"background",
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iuc
parents:
diff changeset
574 "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"background",
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iuc
parents:
diff changeset
575 "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"background",
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iuc
parents:
diff changeset
576 "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"background",
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iuc
parents:
diff changeset
577 "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"background",
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iuc
parents:
diff changeset
578 "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"background",
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iuc
parents:
diff changeset
579 "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"background"
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iuc
parents:
diff changeset
580 }
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
581 },
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iuc
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diff changeset
582 "timers":{
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iuc
parents:
diff changeset
583 "Model fitting":{
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iuc
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diff changeset
584 "order":1,
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iuc
parents:
diff changeset
585 "timer":5
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iuc
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diff changeset
586 },
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iuc
parents:
diff changeset
587 "PRIME analysis":{
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iuc
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diff changeset
588 "order":2,
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iuc
parents:
diff changeset
589 "timer":19
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diff changeset
590 },
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iuc
parents:
diff changeset
591 "Total time":{
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iuc
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diff changeset
592 "order":0,
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iuc
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diff changeset
593 "timer":25
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iuc
parents:
diff changeset
594 }
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
595 }
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
596 }