{
"MLE":{
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},
"headers": [
["alpha;", "Synonymous substitution rate at a site"],
["β-", "Non-synonymous substitution rate at a site for the negative/neutral evolution component"],
["p-", "Mixture distribution weight allocated to β-; loosely -- the proportion of the tree evolving neutrally or under negative selection"],
["β+", "Non-synonymous substitution rate at a site for the positive/neutral evolution component"],
["p+", "Mixture distribution weight allocated to β+; loosely -- the proportion of the tree evolving neutrally or under positive selection"],
["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p+ > 0 and β+ > α"],
["p-value", "Asymptotic p-value for episodic diversification, i.e., p+ > 0 and β+ > α"],
["# branches under selection", "The (very approximate and rough) estimate of how many branches may have been under selection at this site, i.e., had an empirical Bayes factor of 100 or more for the β+ rate"],
["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"],
["MEME LogL", "Site Log-likelihood under the MEME model"],
["FEL LogL", "Site Log-likelihood under the FEL model"]
]
},
"analysis":{
"authors":"Sergei L. Kosakovsky Pond, Steven Weaver",
"citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.",
"contact":"spond@temple.edu",
"info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous\n (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if β+ > α at a site.\n The estimates aggregate information over a proportion of branches at a site,\n so the signal is derived from\n episodic diversification, which is a combination of strength of selection [effect size] and\n the proportion of the tree affected. 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 ",
"requirements":"in-frame codon alignment and a phylogenetic tree",
"version":"2.1.2"
},
"branch attributes":{
"0":{
"Node23":{
"EBF site 102 (partition 1)":1,
"EBF site 103 (partition 1)":1,
"EBF site 112 (partition 1)":1,
"EBF site 118 (partition 1)":1,
"EBF site 119 (partition 1)":1,
"EBF site 12 (partition 1)":0.9834244803905317,
"EBF site 123 (partition 1)":1,
"EBF site 126 (partition 1)":1,
"EBF site 128 (partition 1)":1,
"EBF site 129 (partition 1)":1,
"EBF site 130 (partition 1)":0.9852034436649997,
"EBF site 131 (partition 1)":1,
"EBF site 134 (partition 1)":0.9994375784791201,
"EBF site 136 (partition 1)":1,
"EBF site 138 (partition 1)":1,
"EBF site 14 (partition 1)":1,
"EBF site 18 (partition 1)":1,
"EBF site 32 (partition 1)":1,
"EBF site 38 (partition 1)":1,
"EBF site 51 (partition 1)":1,
"EBF site 63 (partition 1)":1,
"EBF site 64 (partition 1)":0.9876718465393998,
"EBF site 67 (partition 1)":1,
"EBF site 68 (partition 1)":1,
"EBF site 8 (partition 1)":1,
"EBF site 82 (partition 1)":1,
"EBF site 83 (partition 1)":1,
"EBF site 9 (partition 1)":1,
"EBF site 99 (partition 1)":1,
"Global MG94xREV":0.002461279499508527,
"Nucleotide GTR":0.002399192716849548
},
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},
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"Nucleotide GTR":0.004809316882966113,
"original name":"epi_isl_420412_Koersel_20200324_null_1"
},
"epi_isl_420431_Saint_Saulve_20200324_null_3":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"original name":"epi_isl_420431_Saint_Saulve_20200324_null_3"
},
"epi_isl_420450_Sint_Agatha_Berchem_20200307_null_2":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"original name":"epi_isl_420450_Sint_Agatha_Berchem_20200307_null_2"
},
"epi_isl_420482_England_20200318_null_1":{
"Global MG94xREV":0.002405807054408424,
"Nucleotide GTR":0.002403615733834753,
"original name":"epi_isl_420482_England_20200318_null_1"
},
"epi_isl_420484_England_20200319_null_2":{
"Global MG94xREV":0.002411410021222355,
"Nucleotide GTR":0.002408933915895551,
"original name":"epi_isl_420484_England_20200319_null_2"
},
"epi_isl_420852_Kinshasa_20200326_null_4043":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"original name":"epi_isl_420852_Kinshasa_20200326_null_4043"
}
},
"attributes":{
"EBF site 102 (partition 1)":{
"attribute type":"branch label",
"display order":104
},
"EBF site 103 (partition 1)":{
"attribute type":"branch label",
"display order":105
},
"EBF site 112 (partition 1)":{
"attribute type":"branch label",
"display order":114
},
"EBF site 118 (partition 1)":{
"attribute type":"branch label",
"display order":120
},
"EBF site 119 (partition 1)":{
"attribute type":"branch label",
"display order":121
},
"EBF site 12 (partition 1)":{
"attribute type":"branch label",
"display order":14
},
"EBF site 123 (partition 1)":{
"attribute type":"branch label",
"display order":125
},
"EBF site 126 (partition 1)":{
"attribute type":"branch label",
"display order":128
},
"EBF site 128 (partition 1)":{
"attribute type":"branch label",
"display order":130
},
"EBF site 129 (partition 1)":{
"attribute type":"branch label",
"display order":131
},
"EBF site 130 (partition 1)":{
"attribute type":"branch label",
"display order":132
},
"EBF site 131 (partition 1)":{
"attribute type":"branch label",
"display order":133
},
"EBF site 134 (partition 1)":{
"attribute type":"branch label",
"display order":136
},
"EBF site 136 (partition 1)":{
"attribute type":"branch label",
"display order":138
},
"EBF site 138 (partition 1)":{
"attribute type":"branch label",
"display order":140
},
"EBF site 14 (partition 1)":{
"attribute type":"branch label",
"display order":16
},
"EBF site 18 (partition 1)":{
"attribute type":"branch label",
"display order":20
},
"EBF site 32 (partition 1)":{
"attribute type":"branch label",
"display order":34
},
"EBF site 38 (partition 1)":{
"attribute type":"branch label",
"display order":40
},
"EBF site 51 (partition 1)":{
"attribute type":"branch label",
"display order":53
},
"EBF site 63 (partition 1)":{
"attribute type":"branch label",
"display order":65
},
"EBF site 64 (partition 1)":{
"attribute type":"branch label",
"display order":66
},
"EBF site 67 (partition 1)":{
"attribute type":"branch label",
"display order":69
},
"EBF site 68 (partition 1)":{
"attribute type":"branch label",
"display order":70
},
"EBF site 8 (partition 1)":{
"attribute type":"branch label",
"display order":10
},
"EBF site 82 (partition 1)":{
"attribute type":"branch label",
"display order":84
},
"EBF site 83 (partition 1)":{
"attribute type":"branch label",
"display order":85
},
"EBF site 9 (partition 1)":{
"attribute type":"branch label",
"display order":11
},
"EBF site 99 (partition 1)":{
"attribute type":"branch label",
"display order":101
},
"Global MG94xREV":{
"attribute type":"branch length",
"display order":1
},
"Nucleotide GTR":{
"attribute type":"branch length",
"display order":0
},
"original name":{
"attribute type":"node label",
"display order":-1
}
}
},
"data partitions":{
"0":{
"coverage": [
[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]
],
"name":"meme.filter.default"
}
},
"fits":{
"Global MG94xREV":{
"AIC-c":1705.369312624731,
"Equilibrium frequencies": [
[0.02529878484274338],
[0.01258737018390901],
[0.009967019537743167],
[0.03580941055518097],
[0.02134758184536645],
[0.01062145541334168],
[0.008410355147842982],
[0.03021664192224339],
[0.01892437793069474],
[0.009415794157488139],
[0.007455680015752737],
[0.02678669442165064],
[0.01694883440895403],
[0.008432865618542666],
[0.006677370662112003],
[0.02399039216921527],
[0.0160334327018926],
[0.007977408954304129],
[0.006316727779227383],
[0.02269467793808378],
[0.01352930660477965],
[0.006731484995209738],
[0.005330171551723184],
[0.01915018834892545],
[0.01199356972530672],
[0.005967381552014054],
[0.004725133816603274],
[0.01697641467704283],
[0.01074154342039212],
[0.005344437854207465],
[0.004231870178826945],
[0.01520422189160818],
[0.03071537315967425],
[0.0152823850908642],
[0.01210100509943495],
[0.04347637306168295],
[0.025918199095843],
[0.01289555876092641],
[0.01021105157331231],
[0.03668616647175368],
[0.0229761758744204],
[0.01143175978370695],
[0.009051976024400162],
[0.03252185114777016],
[0.02057765923258856],
[0.01023838164121236],
[0.008107026993079506],
[0.02912684748713282],
[0.01282583113193175],
[0.03648780054962477],
[0.02175200028468008],
[0.01082267316496422],
[0.008569684795931542],
[0.03078907992744746],
[0.009594171306040736],
[0.007596923857693875],
[0.02729415391897662],
[0.01726992094744372],
[0.0085926217153735],
[0.00680386985258008],
[0.02444487722658028]
],
"Log Likelihood":-803.1275849162764,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *background*": [
[1.020518490680191, 1]
],
"non-synonymous/synonymous rate ratio for *test*": [
[0, 1]
]
},
"display order":1,
"estimated parameters":49
},
"Nucleotide GTR":{
"AIC-c":1797.468639425677,
"Equilibrium frequencies": [
[0.2780776728145149],
[0.2016044384465437],
[0.2231968810916179],
[0.2971210076473234]
],
"Log Likelihood":-829.3704504948184,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.528765107770809,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":1.439336469898444,
"Substitution rate from nucleotide C to nucleotide G":3.307890276273563,
"Substitution rate from nucleotide C to nucleotide T":8.915071541893553,
"Substitution rate from nucleotide G to nucleotide T":1.795283241275818
},
"display order":0,
"estimated parameters":69
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-04-07/sequences.nsp10.compressed.fas",
"number of sequences":32,
"number of sites":139,
"partition count":1,
"trees":{
"0":"(epi_isl_420484_England_20200319_null_2,epi_isl_417919_Kuala_Lumpur_20200314_null_1,epi_isl_420852_Kinshasa_20200326_null_4043,epi_isl_420052_Ile_de_France_20200320_null_1,epi_isl_416355_Shanghai_20200204_null_2,epi_isl_419917_Victoria_20200320_null_2,epi_isl_411951_Sweden_20200207_null_1,epi_isl_415527_Utrecht_20200312_null_1,epi_isl_420197_South_Yorkshire_20200328_null_1,epi_isl_420364_Anderlecht_20200319_null_1,epi_isl_415477_Netherlands_20200312_null_2,epi_isl_417563_Reykjavik_20200316_null_1,epi_isl_418957_Virginia_20200317_null_1,epi_isl_415593_Washington_20200310_null_1,epi_isl_415652_Bourgogne_France_Comt_20200305_null_1,epi_isl_414934_Shandong_20200121_null_1,epi_isl_416345_Shanghai_20200204_null_1,epi_isl_415699_Switzerland_20200227_null_2,epi_isl_415486_Netherlands_20200313_null_1,(epi_isl_416469_Kessel_Lo_20200303_null_2,epi_isl_420450_Sint_Agatha_Berchem_20200307_null_2,epi_isl_420335_Bierset_20200306_null_1,epi_isl_420431_Saint_Saulve_20200324_null_3)Node23,epi_isl_419245_Hong_Kong_20200222_null_2,epi_isl_415618_Washington_20200309_null_1,epi_isl_419768_Victoria_20200312_null_1,epi_isl_420482_England_20200318_null_1,epi_isl_420198_South_Yorkshire_20200328_null_1,epi_isl_420412_Koersel_20200324_null_1,epi_isl_419496_Wales_20200320_null_2,epi_isl_418398_Finland_20200313_null_2,epi_isl_419249_Hong_Kong_20200225_null_1)"
}
},
"tested":{
"0":{
"Node23":"test",
"epi_isl_411951_Sweden_20200207_null_1":"background",
"epi_isl_414934_Shandong_20200121_null_1":"background",
"epi_isl_415477_Netherlands_20200312_null_2":"background",
"epi_isl_415486_Netherlands_20200313_null_1":"background",
"epi_isl_415527_Utrecht_20200312_null_1":"background",
"epi_isl_415593_Washington_20200310_null_1":"background",
"epi_isl_415618_Washington_20200309_null_1":"background",
"epi_isl_415652_Bourgogne_France_Comt_20200305_null_1":"background",
"epi_isl_415699_Switzerland_20200227_null_2":"background",
"epi_isl_416345_Shanghai_20200204_null_1":"background",
"epi_isl_416355_Shanghai_20200204_null_2":"background",
"epi_isl_416469_Kessel_Lo_20200303_null_2":"background",
"epi_isl_417563_Reykjavik_20200316_null_1":"background",
"epi_isl_417919_Kuala_Lumpur_20200314_null_1":"background",
"epi_isl_418398_Finland_20200313_null_2":"background",
"epi_isl_418957_Virginia_20200317_null_1":"background",
"epi_isl_419245_Hong_Kong_20200222_null_2":"background",
"epi_isl_419249_Hong_Kong_20200225_null_1":"background",
"epi_isl_419496_Wales_20200320_null_2":"background",
"epi_isl_419768_Victoria_20200312_null_1":"background",
"epi_isl_419917_Victoria_20200320_null_2":"background",
"epi_isl_420052_Ile_de_France_20200320_null_1":"background",
"epi_isl_420197_South_Yorkshire_20200328_null_1":"background",
"epi_isl_420198_South_Yorkshire_20200328_null_1":"background",
"epi_isl_420335_Bierset_20200306_null_1":"background",
"epi_isl_420364_Anderlecht_20200319_null_1":"background",
"epi_isl_420412_Koersel_20200324_null_1":"background",
"epi_isl_420431_Saint_Saulve_20200324_null_3":"background",
"epi_isl_420450_Sint_Agatha_Berchem_20200307_null_2":"background",
"epi_isl_420482_England_20200318_null_1":"background",
"epi_isl_420484_England_20200319_null_2":"background",
"epi_isl_420852_Kinshasa_20200326_null_4043":"background"
}
},
"timers":{
"MEME analysis":{
"order":2,
"timer":6
},
"Model fitting":{
"order":1,
"timer":3
},
"Total time":{
"order":0,
"timer":11
}
}
}