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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drhip commit 15c654c3d27df68a47483031961ace7f5b8d998d
author iuc
date Thu, 04 Dec 2025 15:05:26 +0000
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-1:000000000000 0:dd2d60b55e0d
1 {
2 "MLE":{
3 "content":{
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106 },
107 "headers": [
108 ["alpha", "Synonymous substitution rate at a site"],
109 ["beta", "Non-synonymous substitution rate at a site"],
110 ["alpha=beta", "The rate estimate under the neutral model"],
111 ["LRT", "Likelihood ratio test statistic for beta = alpha, versus beta &neq; alpha"],
112 ["p-value", "Asymptotic p-value for evidence of selection, i.e. beta &neq; alpha"],
113 ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
114 ]
115 },
116 "analysis":{
117 "authors":"Sergei L Kosakovsky Pond and Simon DW Frost",
118 "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222",
119 "contact":"spond@temple.edu",
120 "info":"FEL (Fixed Effects Likelihood)\n estimates site-wise synonymous (α) and non-synonymous (β) rates, and\n uses a likelihood ratio test to determine if beta &neq; alpha at a site.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. 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.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis. Version 2.5 adds MH support.\n ",
121 "requirements":"in-frame codon alignment and a phylogenetic tree",
122 "settings":{
123 "ci":0,
124 "multihit":"None",
125 "pvalue":0.1,
126 "resample":0,
127 "site-filter":{
128 "site-filter":null,
129 "site-save-filter":null
130 },
131 "srv":1
132 },
133 "version":"2.5"
134 },
135 "branch attributes":{
136 "0":{
137 "Node2":{
138 "Global MG94xREV":0.01555447631320992,
139 "Nucleotide GTR":0.01391650578382423
140 },
141 "Node3":{
142 "Global MG94xREV":0.007028865074476463,
143 "Nucleotide GTR":0.007313844682570613
144 },
145 "Node8":{
146 "Global MG94xREV":0.006626243690924009,
147 "Nucleotide GTR":0.006196659368038242
148 },
149 "PP563830_1_2023_09_02":{
150 "Global MG94xREV":0,
151 "Nucleotide GTR":1e-06,
152 "original name":"PP563830_1_2023_09_02"
153 },
154 "PP563831_1_2023_08_29":{
155 "Global MG94xREV":0.003308232804180055,
156 "Nucleotide GTR":0.003339882520232537,
157 "original name":"PP563831_1_2023_08_29"
158 },
159 "PP563832_1_2023_08_28":{
160 "Global MG94xREV":0.003305901719100713,
161 "Nucleotide GTR":0.003342518270787742,
162 "original name":"PP563832_1_2023_08_28"
163 },
164 "PP563838_1_2023_09_30":{
165 "Global MG94xREV":0.003316292450534825,
166 "Nucleotide GTR":0.003339882520180704,
167 "original name":"PP563838_1_2023_09_30"
168 },
169 "PP563839_1_2023_09_29":{
170 "Global MG94xREV":0,
171 "Nucleotide GTR":1e-06,
172 "original name":"PP563839_1_2023_09_29"
173 },
174 "PP563845_1_2023_10_22":{
175 "Global MG94xREV":0.005918187425081579,
176 "Nucleotide GTR":0.007157676157708746,
177 "original name":"PP563845_1_2023_10_22"
178 },
179 "PP564823_1_2023_10_06":{
180 "Global MG94xREV":0.04453027608174031,
181 "Nucleotide GTR":0.04195089101557686,
182 "original name":"PP564823_1_2023_10_06"
183 }
184 },
185 "attributes":{
186 "Global MG94xREV":{
187 "attribute type":"branch length",
188 "display order":1
189 },
190 "Nucleotide GTR":{
191 "attribute type":"branch length",
192 "display order":0
193 },
194 "original name":{
195 "attribute type":"node label",
196 "display order":-1
197 }
198 }
199 },
200 "data partitions":{
201 "0":{
202 "coverage": [
203 [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]
204 ],
205 "name":"fel.filter.default"
206 }
207 },
208 "fits":{
209 "Global MG94xREV":{
210 "AIC-c":1098.164180855893,
211 "Equilibrium frequencies": [
212 [0.04022787530103862],
213 [0.01934493712337751],
214 [0.03425741450905353],
215 [0.01425856648080257],
216 [0.03379960463533115],
217 [0.01625368532572285],
218 [0.0287832021345848],
219 [0.01198009852897374],
220 [0.03434841386947805],
221 [0.01651759884459136],
222 [0.02925055929127961],
223 [0.01217462118004102],
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228 [0.01826098626758108],
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232 [0.01534294594175388],
233 [0.007378175514105413],
234 [0.01306580710473399],
235 [0.005438229413926055],
236 [0.01559207164907205],
237 [0.007497976053105356],
238 [0.01327795856827995],
239 [0.005526530758038588],
240 [0.02204519218088164],
241 [0.01060117775101382],
242 [0.01877333269084459],
243 [0.00781380661894053],
244 [0.02001283201397348],
245 [0.009623848489980729],
246 [0.0170426073132688],
247 [0.007093446860043523],
248 [0.01681485300040535],
249 [0.008085991904804354],
250 [0.0143192595888557],
251 [0.005959939409601683],
252 [0.01708787828271292],
253 [0.008217285364372072],
254 [0.0145517635478013],
255 [0.006056711836919557],
256 [0.02416007116849923],
257 [0.01161818898347029],
258 [0.02057432977490965],
259 [0.008563414755540757],
260 [0.01095174735555056],
261 [0.008072200842739543],
262 [0.01913496685581441],
263 [0.009201697278655068],
264 [0.01629503140027161],
265 [0.006782292004731834],
266 [0.009351106613197152],
267 [0.01655961626153459],
268 [0.006892417094094173],
269 [0.02749367841825353],
270 [0.0132212670023302],
271 [0.02341317633368553],
272 [0.009744994946783913]
273 ],
274 "Log Likelihood":-522.0389997890163,
275 "Rate Distributions":{
276 "non-synonymous/synonymous rate ratio for *background*": [
277 [0.2130893675277186, 1]
278 ],
279 "non-synonymous/synonymous rate ratio for *test*": [
280 [0.05367140804417245, 1]
281 ]
282 },
283 "display order":1,
284 "estimated parameters":26
285 },
286 "Nucleotide GTR":{
287 "AIC-c":1130.795872905925,
288 "Equilibrium frequencies": [
289 [0.3347619047619048],
290 [0.2033333333333333],
291 [0.2466666666666667],
292 [0.2152380952380952]
293 ],
294 "Log Likelihood":-546.2152441452704,
295 "Rate Distributions":{
296 "Substitution rate from nucleotide A to nucleotide C":0.1157280802219541,
297 "Substitution rate from nucleotide A to nucleotide G":1,
298 "Substitution rate from nucleotide A to nucleotide T":0,
299 "Substitution rate from nucleotide C to nucleotide G":0.1604122535118794,
300 "Substitution rate from nucleotide C to nucleotide T":2.313607104947681,
301 "Substitution rate from nucleotide G to nucleotide T":0.1528462357734212
302 },
303 "display order":0,
304 "estimated parameters":19
305 }
306 },
307 "input":{
308 "file name":"/home/dcallan-adm/Documents/veg/CAPHEINE/work/66/caf0861a1e46548e7f15d9b82a4920/pretend_DENV1_ref.part_NC_001477.1__capsid_protein_C__95-394_DENV1-nodups.fasta",
309 "number of sequences":7,
310 "number of sites":100,
311 "partition count":1,
312 "trees":{
313 "0":"(PP564823_1_2023_10_06,((PP563832_1_2023_08_28,PP563830_1_2023_09_02,PP563831_1_2023_08_29)Node3,(PP563839_1_2023_09_29,PP563838_1_2023_09_30)Node8)Node2,PP563845_1_2023_10_22)"
314 }
315 },
316 "runtime":"2.5.73",
317 "tested":{
318 "0":{
319 "Node2":"test",
320 "Node3":"test",
321 "Node8":"test",
322 "PP563830_1_2023_09_02":"background",
323 "PP563831_1_2023_08_29":"background",
324 "PP563832_1_2023_08_28":"background",
325 "PP563838_1_2023_09_30":"background",
326 "PP563839_1_2023_09_29":"background",
327 "PP563845_1_2023_10_22":"background",
328 "PP564823_1_2023_10_06":"background"
329 }
330 },
331 "timers":{
332 "FEL analysis":{
333 "order":2,
334 "timer":4
335 },
336 "Model fitting":{
337 "order":1,
338 "timer":1
339 },
340 "Total time":{
341 "order":0,
342 "timer":5
343 }
344 }
345 }