Mercurial > repos > iuc > hyphy_cfel

annotate test-data/summary/nsp8.CFEL.json @ 6:643be54bef90 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 ec5db8349483b2cd46f9da23abe6cefcf65bc714"
author iuc
date Sat, 03 Jul 2021 08:52:57 +0000
parents c046f72e5e3a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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3
c046f72e5e3a "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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iuc
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202 [0, 5.651971820557556, 0, 0, 0, 0, 0.9946823441693979, 1, -1, 0.7022286583320135]
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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parents:
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203 ]
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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204 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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205 "headers": [
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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parents:
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206 ["alpha", "Synonymous substitution rate at a site"],
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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diff changeset
207 ["beta (background)", "Non-synonymous substitution rate at a site for background branches"],
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
208 ["beta (B-1-617)", "Non-synonymous substitution rate at a site for B-1-617 branches"],
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
209 ["beta (Reference)", "Non-synonymous substitution rate at a site for Reference branches"],
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
210 ["subs (B-1-617)", "Substitutions mapped to B-1-617 branches"],
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
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211 ["subs (Reference)", "Substitutions mapped to Reference branches"],
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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parents:
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212 ["P-value (overall)", "P-value for the test that non-synonymous rates differ between any of the selected groups: B-1-617,Reference"],
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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parents:
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213 ["Q-value (overall)", "Q-value for the test that non-synonymous rates differ between any of the selected groups: B-1-617,Reference"],
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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parents:
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214 ["Permutation p-value", "Label permutation test for significant sites"],
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
215 ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale beta-alpha"]
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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parents:
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216 ]
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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parents:
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217 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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parents:
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218 "analysis":{
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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parents:
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219 "authors":"Sergei L Kosakovsky Pond and Steven Weaver",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
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220 "citation":"TBD",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
221 "contact":"spond@temple.edu",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
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222 "help":"http://www.hyphy.org/methods/other/contrast-fel/",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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223 "info":"Contrast-FEL (Fixed Effects Likelihood) investigates whether or not selective pressures differ between two or more sets of\n branches at a site. Site-specific synonymous (alpha) and non-synonymous (beta, one per branch set) substitution rates are estimated\n and then beta rates are tested for equality at each site. LRT and permutation tests ar used to assess significance at each site, and FDR is applied alignment wide to call sites with different selective profiles",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
224 "requirements":"in-frame codon alignment and a phylogenetic tree; only single partition data are supported",
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iuc
parents:
diff changeset
225 "version":"0.5"
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iuc
parents:
diff changeset
226 },
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iuc
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diff changeset
227 "branch attributes":{
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iuc
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diff changeset
228 "0":{
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iuc
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diff changeset
229 "Node20":{
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iuc
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diff changeset
230 "Global MG94xREV":0.001634892186392535,
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iuc
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diff changeset
231 "Nucleotide GTR":0.001684521619549293
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iuc
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diff changeset
232 },
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iuc
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diff changeset
233 "Node38":{
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iuc
parents:
diff changeset
234 "Global MG94xREV":0.001919664151147453,
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iuc
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diff changeset
235 "Nucleotide GTR":0.00168484920326581
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iuc
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diff changeset
236 },
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iuc
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diff changeset
237 "Node4":{
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iuc
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diff changeset
238 "Global MG94xREV":0.001634608725470079,
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iuc
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diff changeset
239 "Nucleotide GTR":0.001683801387489096
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iuc
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diff changeset
240 },
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iuc
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diff changeset
241 "REFERENCE":{
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iuc
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diff changeset
242 "Global MG94xREV":0,
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iuc
parents:
diff changeset
243 "Nucleotide GTR":0,
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iuc
parents:
diff changeset
244 "original name":"REFERENCE"
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iuc
parents:
diff changeset
245 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
246 "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{
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iuc
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diff changeset
247 "Global MG94xREV":0,
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iuc
parents:
diff changeset
248 "Nucleotide GTR":0,
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iuc
parents:
diff changeset
249 "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021"
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iuc
parents:
diff changeset
250 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
251 "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{
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iuc
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diff changeset
252 "Global MG94xREV":0.001728428286527107,
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iuc
parents:
diff changeset
253 "Nucleotide GTR":0.001682745450340891,
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iuc
parents:
diff changeset
254 "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021"
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iuc
parents:
diff changeset
255 },
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iuc
parents:
diff changeset
256 "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{
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iuc
parents:
diff changeset
257 "Global MG94xREV":0,
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iuc
parents:
diff changeset
258 "Nucleotide GTR":0,
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iuc
parents:
diff changeset
259 "original name":"epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021"
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iuc
parents:
diff changeset
260 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
261 "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{
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iuc
parents:
diff changeset
262 "Global MG94xREV":0.001727412680411063,
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iuc
parents:
diff changeset
263 "Nucleotide GTR":0.00168274558227101,
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iuc
parents:
diff changeset
264 "original name":"epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021"
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iuc
parents:
diff changeset
265 },
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iuc
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diff changeset
266 "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":{
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iuc
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diff changeset
267 "Global MG94xREV":0.001731169192232254,
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iuc
parents:
diff changeset
268 "Nucleotide GTR":0.001684401404203384,
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iuc
parents:
diff changeset
269 "original name":"epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021"
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iuc
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diff changeset
270 },
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iuc
parents:
diff changeset
271 "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{
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iuc
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diff changeset
272 "Global MG94xREV":0.001728394297110263,
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iuc
parents:
diff changeset
273 "Nucleotide GTR":0.00168406792173386,
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iuc
parents:
diff changeset
274 "original name":"epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021"
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iuc
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diff changeset
275 },
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iuc
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diff changeset
276 "epi_isl_1543980_hCoV_19_Singapore_490_2021":{
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iuc
parents:
diff changeset
277 "Global MG94xREV":0.001731480337658913,
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iuc
parents:
diff changeset
278 "Nucleotide GTR":0.001684975469042935,
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iuc
parents:
diff changeset
279 "original name":"epi_isl_1543980/hCoV-19/Singapore/490/2021"
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iuc
parents:
diff changeset
280 },
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iuc
parents:
diff changeset
281 "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":{
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iuc
parents:
diff changeset
282 "Global MG94xREV":0.00173257034392943,
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iuc
parents:
diff changeset
283 "Nucleotide GTR":0.001684401583391051,
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iuc
parents:
diff changeset
284 "original name":"epi_isl_1544068/hCoV-19/India/MH-NCCS-RT231527/2021"
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iuc
parents:
diff changeset
285 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
286 "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":{
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iuc
parents:
diff changeset
287 "Global MG94xREV":0.001728428527066194,
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iuc
parents:
diff changeset
288 "Nucleotide GTR":0.001682745512695379,
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iuc
parents:
diff changeset
289 "original name":"epi_isl_1573247/hCoV-19/Germany/un-RKI-I-068985/2021"
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iuc
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diff changeset
290 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
291 "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":{
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iuc
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diff changeset
292 "Global MG94xREV":0,
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iuc
parents:
diff changeset
293 "Nucleotide GTR":0,
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iuc
parents:
diff changeset
294 "original name":"epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021"
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iuc
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diff changeset
295 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
296 "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":{
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iuc
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diff changeset
297 "Global MG94xREV":0.001730278969738805,
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iuc
parents:
diff changeset
298 "Nucleotide GTR":0.001684431017860219,
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iuc
parents:
diff changeset
299 "original name":"epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021"
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iuc
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diff changeset
300 },
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iuc
parents:
diff changeset
301 "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":{
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iuc
parents:
diff changeset
302 "Global MG94xREV":0.00173028305819776,
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iuc
parents:
diff changeset
303 "Nucleotide GTR":0.001684439221071522,
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iuc
parents:
diff changeset
304 "original name":"epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021"
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iuc
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diff changeset
305 },
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iuc
parents:
diff changeset
306 "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":{
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iuc
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diff changeset
307 "Global MG94xREV":0,
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iuc
parents:
diff changeset
308 "Nucleotide GTR":0,
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iuc
parents:
diff changeset
309 "original name":"epi_isl_1615709/hCoV-19/England/CAMC-14E792B/2021"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
310 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
311 "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":{
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iuc
parents:
diff changeset
312 "Global MG94xREV":0.001732590473818113,
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iuc
parents:
diff changeset
313 "Nucleotide GTR":0.00168443927661716,
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iuc
parents:
diff changeset
314 "original name":"epi_isl_1632256/hCoV-19/England/RAND-14E1D70/2021"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
315 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
316 "epi_isl_1652105_hCoV_19_Singapore_561_2021":{
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iuc
parents:
diff changeset
317 "Global MG94xREV":0.001730912440099921,
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iuc
parents:
diff changeset
318 "Nucleotide GTR":0.001685171120971631,
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iuc
parents:
diff changeset
319 "original name":"epi_isl_1652105/hCoV-19/Singapore/561/2021"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
320 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
321 "epi_isl_1652118_hCoV_19_Singapore_575_2021":{
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iuc
parents:
diff changeset
322 "Global MG94xREV":0.00173012682288667,
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iuc
parents:
diff changeset
323 "Nucleotide GTR":0.001684401899924961,
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iuc
parents:
diff changeset
324 "original name":"epi_isl_1652118/hCoV-19/Singapore/575/2021"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
325 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
326 "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
327 "Global MG94xREV":0.01048097604892967,
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iuc
parents:
diff changeset
328 "Nucleotide GTR":0.01020457779555702,
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iuc
parents:
diff changeset
329 "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
330 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
331 "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
332 "Global MG94xREV":0.02680857534231693,
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iuc
parents:
diff changeset
333 "Nucleotide GTR":0.02592331511084145,
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iuc
parents:
diff changeset
334 "original name":"gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
335 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
336 "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
337 "Global MG94xREV":0.005248107108130198,
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iuc
parents:
diff changeset
338 "Nucleotide GTR":0.005093980037543817,
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iuc
parents:
diff changeset
339 "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"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
340 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
341 "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
342 "Global MG94xREV":0.003471698044100598,
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iuc
parents:
diff changeset
343 "Nucleotide GTR":0.003379296026417724,
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
344 "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"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
345 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
346 "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
347 "Global MG94xREV":0.003457568777482139,
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iuc
parents:
diff changeset
348 "Nucleotide GTR":0.003372774424630234,
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
349 "original name":"gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
350 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
351 "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
352 "Global MG94xREV":0.003467133892779525,
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iuc
parents:
diff changeset
353 "Nucleotide GTR":0.003374190595560375,
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iuc
parents:
diff changeset
354 "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"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
355 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
356 "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
357 "Global MG94xREV":0.005201716586138184,
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iuc
parents:
diff changeset
358 "Nucleotide GTR":0.00505933790460295,
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iuc
parents:
diff changeset
359 "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"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
360 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
361 "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
362 "Global MG94xREV":0.003459439643420186,
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iuc
parents:
diff changeset
363 "Nucleotide GTR":0.003373764235314068,
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iuc
parents:
diff changeset
364 "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"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
365 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
366 "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
367 "Global MG94xREV":0.005223283115211614,
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iuc
parents:
diff changeset
368 "Nucleotide GTR":0.005068409188375663,
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
369 "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"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
370 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
371 "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
372 "Global MG94xREV":0.003458770062029164,
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iuc
parents:
diff changeset
373 "Nucleotide GTR":0.003372774424770855,
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
374 "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"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
375 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
376 "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
377 "Global MG94xREV":0.001732985724599283,
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
378 "Nucleotide GTR":0.001686266012390882,
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iuc
parents:
diff changeset
379 "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"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
380 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
381 "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
382 "Global MG94xREV":0.003473875423912177,
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iuc
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diff changeset
383 "Nucleotide GTR":0.003374436490976879,
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iuc
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diff changeset
384 "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"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
385 },
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iuc
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diff changeset
386 "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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diff changeset
387 "Global MG94xREV":0.003465962442102671,
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iuc
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diff changeset
388 "Nucleotide GTR":0.003376034743011948,
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iuc
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diff changeset
389 "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
390 },
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iuc
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diff changeset
391 "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
392 "Global MG94xREV":0.003468563557182978,
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iuc
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diff changeset
393 "Nucleotide GTR":0.003374190741831846,
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iuc
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diff changeset
394 "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
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diff changeset
395 },
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iuc
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diff changeset
396 "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
397 "Global MG94xREV":0.003465082984487299,
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iuc
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diff changeset
398 "Nucleotide GTR":0.003376937492543959,
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iuc
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diff changeset
399 "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
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diff changeset
400 }
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iuc
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diff changeset
401 },
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iuc
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diff changeset
402 "attributes":{
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iuc
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diff changeset
403 "Global MG94xREV":{
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diff changeset
404 "attribute type":"branch length",
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diff changeset
405 "display order":1
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406 },
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iuc
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diff changeset
407 "Nucleotide GTR":{
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iuc
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diff changeset
408 "attribute type":"branch length",
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409 "display order":0
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iuc
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410 },
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iuc
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diff changeset
411 "original name":{
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iuc
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diff changeset
412 "attribute type":"node label",
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diff changeset
413 "display order":-1
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diff changeset
414 }
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diff changeset
415 }
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416 },
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diff changeset
417 "data partitions":{
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418 "0":{
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419 "coverage": [
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diff changeset
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c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
421 ],
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diff changeset
422 "name":"fel.filter.default"
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parents:
diff changeset
423 }
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424 },
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425 "fits":{
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parents:
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426 "Global MG94xREV":{
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diff changeset
427 "AIC-c":2512.992528252278,
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diff changeset
428 "Equilibrium frequencies": [
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iuc
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diff changeset
491 "Log Likelihood":-1204.057620166247,
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492 "Rate Distributions":{
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iuc
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493 "non-synonymous/synonymous rate ratio for *B-1-617*": [
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diff changeset
494 [21.18256593595067, 1]
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495 ],
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496 "non-synonymous/synonymous rate ratio for *Reference*": [
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497 [0, 1]
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499 "non-synonymous/synonymous rate ratio for *background*": [
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501 ]
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502 },
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503 "display order":1,
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504 "estimated parameters":52
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505 },
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diff changeset
506 "Nucleotide GTR":{
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diff changeset
507 "AIC-c":2633.0046471406,
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508 "Equilibrium frequencies": [
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513 ],
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514 "Log Likelihood":-1247.247280799152,
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515 "Rate Distributions":{
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iuc
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diff changeset
516 "Substitution rate from nucleotide A to nucleotide C":0,
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iuc
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diff changeset
517 "Substitution rate from nucleotide A to nucleotide G":1,
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iuc
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diff changeset
518 "Substitution rate from nucleotide A to nucleotide T":0.3101631549852981,
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iuc
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diff changeset
519 "Substitution rate from nucleotide C to nucleotide G":1.129990583516242,
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iuc
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520 "Substitution rate from nucleotide C to nucleotide T":2.723444388603395,
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iuc
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diff changeset
521 "Substitution rate from nucleotide G to nucleotide T":1.720896006888861
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522 },
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iuc
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523 "display order":0,
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iuc
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diff changeset
524 "estimated parameters":69
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525 }
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526 },
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527 "input":{
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diff changeset
528 "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
529 "number of sequences":32,
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iuc
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diff changeset
530 "number of sites":198,
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531 "partition count":1,
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532 "trees":{
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iuc
parents:
diff changeset
533 "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)"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
534 }
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
535 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
536 "tested":{
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iuc
parents:
diff changeset
537 "0":{
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iuc
parents:
diff changeset
538 "Node20":"B-1-617",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
539 "Node38":"Reference",
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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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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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iuc
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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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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
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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
561 "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
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diff changeset
562 "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
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diff changeset
563 "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
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diff changeset
564 "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
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diff changeset
565 "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
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diff changeset
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iuc
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diff changeset
567 "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
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diff changeset
568 "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
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diff changeset
569 "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
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diff changeset
570 "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
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diff changeset
571 "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
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diff changeset
572 "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
573 }
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
574 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
575 "timers":{
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iuc
parents:
diff changeset
576 "FEL analysis":{
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iuc
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diff changeset
577 "order":2,
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iuc
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diff changeset
578 "timer":9
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iuc
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diff changeset
579 },
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iuc
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diff changeset
580 "Model fitting":{
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iuc
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diff changeset
581 "order":1,
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iuc
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diff changeset
582 "timer":5
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iuc
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diff changeset
583 },
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iuc
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diff changeset
584 "Total time":{
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iuc
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diff changeset
585 "order":0,
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iuc
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586 "timer":14
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iuc
parents:
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587 }
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
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588 }
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
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589 }