annotate test-data/summary/nsp8.MEME.json @ 29:31e1a5940620 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 9fa2234b56facaf70fce12e5c60638d801997594"

{
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      ]
    },
   "headers":    [
["alpha;", "Synonymous substitution rate at a site"],
    ["&beta;<sup>-</sup>", "Non-synonymous substitution rate at a site for the negative/neutral evolution component"],
    ["p<sup>-</sup>", "Mixture distribution weight allocated to &beta;<sup>-</sup>; loosely -- the proportion of the tree evolving neutrally or under negative selection"],
    ["&beta;<sup>+</sup>", "Non-synonymous substitution rate at a site for the positive/neutral evolution component"],
    ["p<sup>+</sup>", "Mixture distribution weight allocated to &beta;<sup>+</sup>; loosely -- the proportion of the tree evolving neutrally or under positive selection"],
    ["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p<sup>+</sup> &gt; 0 <emph>and<emph> &beta;<sup>+</sup> &gt; &alpha;"],
    ["p-value", "Asymptotic p-value for episodic diversification, i.e., p<sup>+</sup> &gt; 0 <emph>and<emph> &beta;<sup>+</sup> &gt; &alpha;"],
    ["# 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 &beta;<sup>+</sup> 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":"[e-mail]",
   "info":"MEME (Mixed Effects Model of Evolution)\n    estimates a site-wise synonymous (&alpha;) and a two-category mixture of non-synonymous\n    (&beta;-, with proportion p-, and &beta;+ with proportion [1-p-]) rates, and\n    uses a likelihood ratio test to determine if &beta;+ > &alpha; 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":{
     "Node20":{
       "EBF site 101 (partition 1)":1,
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       "EBF site 83 (partition 1)":1,
       "EBF site 85 (partition 1)":0.9998334064611279,
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     "REFERENCE":{
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     "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":{
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     "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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     "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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     "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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     "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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     "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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     "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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     "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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     "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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     "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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       "original name":"gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human"
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     "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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       "original name":"gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human"
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     "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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     "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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       "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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     "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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     "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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     "EBF site 103 (partition 1)":{
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     "EBF site 99 (partition 1)":{
       "attribute type":"branch label",
       "display order":200
      },
     "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, 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] 
      ],
     "name":"meme.filter.default"
    }
  },
 "fits":{
   "Global MG94xREV":{
     "AIC-c":2512.962001126494,
     "Equilibrium frequencies":      [
[0.03825952761243274],
      [0.01370948533169502],
      [0.0238326285579188],
      [0.05169206288834598],
      [0.02910782227384961],
      [0.01043016700423795],
      [0.01813184740308045],
      [0.03932728586627101],
      [0.01035067712195123],
      [0.003708944282165923],
      [0.006447644771501305],
      [0.01398469573761802],
      [0.0283653688047424],
      [0.01016412464618009],
      [0.01766935821790241],
      [0.03832416445281453],
      [0.01521889661505549],
      [0.005453366858635389],
      [0.009480156518454269],
      [0.02056209812326697],
      [0.01157852606970437],
      [0.004148917752546374],
      [0.007212496554133422],
      [0.01564363009947405],
      [0.00411729822204095],
      [0.001475345962268018],
      [0.002564747797779777],
      [0.005562840210150803],
      [0.01128319250724396],
      [0.004043091272315801],
      [0.007028527343480687],
      [0.01524460789411934],
      [0.03592403244011121],
      [0.01287261047188149],
      [0.02237780168434643],
      [0.04853659885475865],
      [0.02733097915424774],
      [0.009793473186905268],
      [0.01702501611901085],
      [0.03692661100139533],
      [0.009718835644621534],
      [0.003482537371104292],
      [0.0060540580187001],
      [0.01313102107355921],
      [0.02663384763763138],
      [0.009543670983435077],
      [0.01659075888876379],
      [0.0359847236220365],
      [0.00848480075962617],
      [0.03199221880690793],
      [0.01801483181642438],
      [0.006455230577911434],
      [0.01122180073845716],
      [0.02433965804833868],
      [0.002295465694104339],
      [0.003990447484454917],
      [0.008655128485630147],
      [0.01755532734880559],
      [0.00629057695692368],
      [0.01093556617204019],
      [0.02371882618448924] 
      ],
     "Log Likelihood":-1205.058976374832,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *background*":        [
[0.4929148115209321, 1] 
        ],
       "non-synonymous/synonymous rate ratio for *test*":        [
[24.31954771499909, 1] 
        ]
      },
     "display order":1,
     "estimated parameters":51
    },
   "Nucleotide GTR":{
     "AIC-c":2633.0046471406,
     "Equilibrium frequencies":      [
[0.3251262626262627],
      [0.1799242424242424],
      [0.2026515151515151],
      [0.2922979797979798] 
      ],
     "Log Likelihood":-1247.247280799152,
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0.3101631549852981,
       "Substitution rate from nucleotide C to nucleotide G":1.129990583516242,
       "Substitution rate from nucleotide C to nucleotide T":2.723444388603395,
       "Substitution rate from nucleotide G to nucleotide T":1.720896006888861
      },
     "display order":0,
     "estimated parameters":69
    }
  },
 "input":{
   "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas",
   "number of sequences":32,
   "number of sites":198,
   "partition count":1,
   "trees":{
     "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)"
    }
  },
 "tested":{
   "0":{
     "Node20":"test",
     "Node38":"background",
     "Node4":"test",
     "REFERENCE":"background",
     "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"background",
     "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"background",
     "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"background",
     "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"background",
     "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"background",
     "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"background",
     "epi_isl_1543980_hCoV_19_Singapore_490_2021":"background",
     "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"background",
     "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"background",
     "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"background",
     "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"background",
     "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"background",
     "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"background",
     "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"background",
     "epi_isl_1652105_hCoV_19_Singapore_561_2021":"background",
     "epi_isl_1652118_hCoV_19_Singapore_575_2021":"background",
     "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"background",
     "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"background",
     "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"background",
     "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",
     "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"background",
     "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",
     "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",
     "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",
     "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":"background",
     "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",
     "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",
     "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",
     "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",
     "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",
     "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"
    }
  },
 "timers":{
   "MEME analysis":{
     "order":2,
     "timer":5
    },
   "Model fitting":{
     "order":1,
     "timer":5
    },
   "Total time":{
     "order":0,
     "timer":10
    }
  }
}