annotate test-data/FEL/gene2.json @ 0:dd2d60b55e0d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drhip commit 15c654c3d27df68a47483031961ace7f5b8d998d

{
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   "headers":    [
["alpha", "Synonymous substitution rate at a site"],
    ["beta", "Non-synonymous substitution rate at a site"],
    ["alpha=beta", "The rate estimate under the neutral model"],
    ["LRT", "Likelihood ratio test statistic for beta = alpha, versus beta &neq; alpha"],
    ["p-value", "Asymptotic p-value for evidence of selection, i.e. beta &neq; alpha"],
    ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
    ]
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 "analysis":{
   "authors":"Sergei L Kosakovsky Pond and Simon DW Frost",
   "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",
   "contact":"[e-mail]",
   "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    ",
   "requirements":"in-frame codon alignment and a phylogenetic tree",
   "settings":{
     "ci":0,
     "multihit":"None",
     "pvalue":0.1,
     "resample":0,
     "site-filter":{
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       "site-save-filter":null
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     "srv":1
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   "version":"2.5"
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       "original name":"PP563830_1_2023_09_02"
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     "original name":{
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     "name":"fel.filter.default"
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     "Log Likelihood":-522.0389997890163,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *background*":        [
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       "non-synonymous/synonymous rate ratio for *test*":        [
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     "display order":1,
     "estimated parameters":26
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     "Log Likelihood":-546.2152441452704,
     "Rate Distributions":{
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       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0,
       "Substitution rate from nucleotide C to nucleotide G":0.1604122535118794,
       "Substitution rate from nucleotide C to nucleotide T":2.313607104947681,
       "Substitution rate from nucleotide G to nucleotide T":0.1528462357734212
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     "display order":0,
     "estimated parameters":19
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   "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",
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 "runtime":"2.5.73",
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     "Node8":"test",
     "PP563830_1_2023_09_02":"background",
     "PP563831_1_2023_08_29":"background",
     "PP563832_1_2023_08_28":"background",
     "PP563838_1_2023_09_30":"background",
     "PP563839_1_2023_09_29":"background",
     "PP563845_1_2023_10_22":"background",
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 "timers":{
   "FEL analysis":{
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     "timer":4
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   "Model fitting":{
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     "timer":1
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   "Total time":{
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}