Mercurial > repos > iuc > hyphy_absrel

comparison test-data/summary/nsp8.combined.fas.BGM.json @ 27:8633ea985719 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 00684bab4c9e740cfa6a39abc444380e6818fd97"
author iuc
date Wed, 09 Jun 2021 07:04:45 +0000
parents
children
comparison
equal deleted inserted replaced
26:5f2ca10db92a 27:8633ea985719
1 {
2 "analysis":{
3 "authors":"Art FY Poon, Fraser I Lewis, Simon DW Frost and Sergei L Kosakovsky Pond",
4 "citation":"Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models (2008). _Bioinformatics_ 24(17): 1949-1950",
5 "contact":"apoon42@uwo.ca",
6 "info":"BGM (Bayesian Graphical Model) uses a maximum likelihood ancestral state reconstruction to\nmap substitution (non-synonymous only for coding data) events to branches in the\nphylogeny and then analyzes the joint distribution of the\nsubstitution map using a Bayesian graphical model (network).\nNext, a Markov chain Monte Carlo analysis is used to generate\na random sample of network structures from the posterior\ndistribution given the data. Each node in the network\nrepresents a codon site in the alignment, and links (edges)\nbetween nodes indicate high posterior support for correlated\nsubstitutions at the two sites over time, which implies coevolution.",
7 "requirements":"in-frame codon alignment and a phylogenetic tree",
8 "version":"1.2"
9 },
10 "branch attributes":{
11 "0":{
12 "Node10":{
13 "models.codon.MG_REV.ModelDescription":0
14 },
15 "Node12":{
16 "models.codon.MG_REV.ModelDescription":0
17 },
18 "Node13":{
19 "models.codon.MG_REV.ModelDescription":0
20 },
21 "Node16":{
22 "models.codon.MG_REV.ModelDescription":0
23 },
24 "Node19":{
25 "models.codon.MG_REV.ModelDescription":0
26 },
27 "Node2":{
28 "models.codon.MG_REV.ModelDescription":0
29 },
30 "Node20":{
31 "models.codon.MG_REV.ModelDescription":0.001732564301319626
32 },
33 "Node23":{
34 "models.codon.MG_REV.ModelDescription":0
35 },
36 "Node24":{
37 "models.codon.MG_REV.ModelDescription":0
38 },
39 "Node27":{
40 "models.codon.MG_REV.ModelDescription":0
41 },
42 "Node28":{
43 "models.codon.MG_REV.ModelDescription":0
44 },
45 "Node29":{
46 "models.codon.MG_REV.ModelDescription":0
47 },
48 "Node3":{
49 "models.codon.MG_REV.ModelDescription":0
50 },
51 "Node30":{
52 "models.codon.MG_REV.ModelDescription":0
53 },
54 "Node33":{
55 "models.codon.MG_REV.ModelDescription":0
56 },
57 "Node34":{
58 "models.codon.MG_REV.ModelDescription":0
59 },
60 "Node35":{
61 "models.codon.MG_REV.ModelDescription":0
62 },
63 "Node36":{
64 "models.codon.MG_REV.ModelDescription":0
65 },
66 "Node38":{
67 "models.codon.MG_REV.ModelDescription":0.001730721769143463
68 },
69 "Node4":{
70 "models.codon.MG_REV.ModelDescription":0.001731994998894883
71 },
72 "Node40":{
73 "models.codon.MG_REV.ModelDescription":0
74 },
75 "Node43":{
76 "models.codon.MG_REV.ModelDescription":0
77 },
78 "Node44":{
79 "models.codon.MG_REV.ModelDescription":0
80 },
81 "Node47":{
82 "models.codon.MG_REV.ModelDescription":0
83 },
84 "Node50":{
85 "models.codon.MG_REV.ModelDescription":0
86 },
87 "Node54":{
88 "models.codon.MG_REV.ModelDescription":0
89 },
90 "Node57":{
91 "models.codon.MG_REV.ModelDescription":0
92 },
93 "Node58":{
94 "models.codon.MG_REV.ModelDescription":0
95 },
96 "Node8":{
97 "models.codon.MG_REV.ModelDescription":0
98 },
99 "REFERENCE":{
100 "models.codon.MG_REV.ModelDescription":0
101 },
102 "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{
103 "models.codon.MG_REV.ModelDescription":0
104 },
105 "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{
106 "models.codon.MG_REV.ModelDescription":0.001729346788706704
107 },
108 "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{
109 "models.codon.MG_REV.ModelDescription":0
110 },
111 "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{
112 "models.codon.MG_REV.ModelDescription":0.001726770081665013
113 },
114 "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":{
115 "models.codon.MG_REV.ModelDescription":0.001730890984495782
116 },
117 "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{
118 "models.codon.MG_REV.ModelDescription":0.001729521179312332
119 },
120 "epi_isl_1543980_hCoV_19_Singapore_490_2021":{
121 "models.codon.MG_REV.ModelDescription":0.00173187799003057
122 },
123 "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":{
124 "models.codon.MG_REV.ModelDescription":0.001731880362018201
125 },
126 "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":{
127 "models.codon.MG_REV.ModelDescription":0.001729347411994937
128 },
129 "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":{
130 "models.codon.MG_REV.ModelDescription":0
131 },
132 "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":{
133 "models.codon.MG_REV.ModelDescription":0.001731050783674516
134 },
135 "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":{
136 "models.codon.MG_REV.ModelDescription":0.001731182381236102
137 },
138 "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":{
139 "models.codon.MG_REV.ModelDescription":0
140 },
141 "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":{
142 "models.codon.MG_REV.ModelDescription":0.001732532467960361
143 },
144 "epi_isl_1652105_hCoV_19_Singapore_561_2021":{
145 "models.codon.MG_REV.ModelDescription":0.001730310938171899
146 },
147 "epi_isl_1652118_hCoV_19_Singapore_575_2021":{
148 "models.codon.MG_REV.ModelDescription":0.001730892114618073
149 },
150 "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":{
151 "models.codon.MG_REV.ModelDescription":0.010477277172687
152 },
153 "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":{
154 "models.codon.MG_REV.ModelDescription":0.0267904473393482
155 },
156 "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":{
157 "models.codon.MG_REV.ModelDescription":0.005246785993713827
158 },
159 "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":{
160 "models.codon.MG_REV.ModelDescription":0.003470769604618349
161 },
162 "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":{
163 "models.codon.MG_REV.ModelDescription":0.003457492024366724
164 },
165 "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":{
166 "models.codon.MG_REV.ModelDescription":0.003467086067652968
167 },
168 "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":{
169 "models.codon.MG_REV.ModelDescription":0.005199945527312524
170 },
171 "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":{
172 "models.codon.MG_REV.ModelDescription":0.003459351766803247
173 },
174 "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":{
175 "models.codon.MG_REV.ModelDescription":0.0052232197685525
176 },
177 "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":{
178 "models.codon.MG_REV.ModelDescription":0.003458730279363404
179 },
180 "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":{
181 "models.codon.MG_REV.ModelDescription":0.001734049878603634
182 },
183 "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":{
184 "models.codon.MG_REV.ModelDescription":0.003472162792845677
185 },
186 "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":{
187 "models.codon.MG_REV.ModelDescription":0.003466781435751312
188 },
189 "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":{
190 "models.codon.MG_REV.ModelDescription":0.003467395894648151
191 },
192 "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":{
193 "models.codon.MG_REV.ModelDescription":0.003463960996259906
194 }
195 },
196 "attributes":{
197 "models.codon.MG_REV.ModelDescription":{
198 "attribute type":"branch length",
199 "display order":0
200 }
201 }
202 },
203 "data partitions":{
204 "0":{
205 "coverage": [
206 [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]
207 ],
208 "name":"bgm.filter.default"
209 }
210 },
211 "fits":{
212 "models.codon.MG_REV.ModelDescription":{
213 "AIC-c":2565.76651309329,
214 "Log Likelihood":-1205.948282908683,
215 "Rate Distributions":null,
216 "display order":0,
217 "estimated parameters":76
218 }
219 },
220 "input":{
221 "datatype":"codon",
222 "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas",
223 "number of sequences":32,
224 "number of sites":198,
225 "trees":{
226 "0":"((((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)Node3,(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)Node13,(epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)Node16)Node12)Node10)Node8)Node2,((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)Node24,((((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)Node30,((((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)Node40)Node38)Node36,((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)Node44,(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)Node47)Node43)Node35,(epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021,epi_isl_1543980_hCoV_19_Singapore_490_2021)Node50)Node34,epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021)Node33)Node29,(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)Node54)Node28,((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)Node58,epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021)Node57)Node27)Node23)Node19,REFERENCE)"
227 }
228 },
229 "settings":{
230 "burn-in":10000,
231 "data-type":"codon",
232 "max-parents":1,
233 "min-subs":1,
234 "samples":100,
235 "steps":100000,
236 "threshold":0.5
237 },
238 "tested":0,
239 "timers":{
240 "Baseline fit":{
241 "order":1,
242 "timer":4
243 },
244 "Network inference":{
245 "order":2,
246 "timer":0
247 },
248 "Overall":{
249 "order":0,
250 "timer":4
251 }
252 }
253 }