Mercurial > repos > iuc > hyphy_fubar

{
 "MLE":{
   "content":{
     "0":      [
[0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [3.195197959507056, 0, 3.205811877302111, 0.002772105520872259, 0.9580101497567953, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, -7.296727429917382e-05, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [3.238107125504523, 0, 3.213547473340999, 0.003030822331904659, 0.9560963156973498, 0],
      [0, 1.332038499257686, 0, -0.001332719656321757, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [6.598685982136248, 0.2251722656465092, 6.592228961936009, 0.005547079257077314, 0.9406294756580599, 0],
      [0, 0, 0, -2.674095220811523e-06, 1, 0],
      [6.598685982136248, 0.2251722656465092, 6.592228961936009, 0.005547079257077314, 0.9406294756580599, 0],
      [0, 0, 0, 0, 1, 0],
      [6.158743797064303, 0.2592752451004765, 6.174124078617361, 0.005128927725017718, 0.9429070828447497, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 1.212374231203373, 0, -0.001087198701075209, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, -3.905098004963747e-07, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [6.138362004166043, 0.2445181781691473, 6.130401353642858, 0.005133217856357675, 0.9428832507411992, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0.5381482959007637, 0, -0.000478648432334694, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [20.56274947956719, 1.153771012915874, 20.31835550563158, 0.01485544411855955, 0.9029917493640262, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [12.332534670739, 3469.599471446826, 25.80735991393082, 7.940542096376955, 0.004833935152283808, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, -1.482836388788655e-06, 1, 0],
      [15.47421552854267, 0.1366859327111816, 15.4417258929309, 0.01080363925394323, 0.9172165220913007, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 1.464737792323401, 0, -0.001659709283721611, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [6.138362004166043, 0.2445181781691473, 6.130401363029468, 0.005133279629863097, 0.9428829076563918, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, -6.884674199625351e-07, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [10000, 0.0600875449979046, 0, 0.8876016225813821, 0.3461280740416711, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [15.57863687176358, 0.14470798181776, 15.40388468507432, 0.01200895125781898, 0.9127382212825174, 0],
      [0, 0.3002103330212254, 0, -0.0003012569440272728, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, -5.985593496404817e-07, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, -6.061155737313584e-06, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 1.362355024782405, 0, -0.00131370882900228, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, -5.257292201577002e-07, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, -4.991814819277351e-07, 1, 0],
      [0, 0, 0, -7.833423893544023e-06, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, -8.039429992834357e-07, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [20.6095871795339, 0.1628160803464207, 20.15787307208067, 0.01558872262298117, 0.9006384977726481, 0],
      [0, 0, 0, 0, 1, 0],
      [20.59856903939906, 0.1617801981930136, 20.11290486801385, 0.01562182837507642, 0.9005335944549532, 0],
      [0, 0, 0, 0, 1, 0],
      [3.204827658624908, 0, 3.187337223213465, 0.003168153989062006, 0.9551136871116382, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [3.204827658624908, 0, 3.187370131670412, 0.002886343089862464, 0.9571545056926204, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, -2.168215438302923e-06, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0.07142484547739002, 0.001095427010571795, 8.650918134556207e-05, 0.9925789578064024, 0],
      [0, 1.586299161132937, 0, -0.001422640320104307, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [5.156731298985191, 0.1836495062523509, 5.148556007804233, 0.003621766693342465, 0.952011385899849, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 2693.39646102285, 14.33106133022015, 10.37651206398012, 0.001276285779958086, 0],
      [0, 0, 0, -2.269114039599174e-05, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, -2.784096764685273e-06, 1, 0],
      [3.923451006078712, 0.1318813648872235, 3.887276534899457, 0.002190196830113678, 0.9626729966348267, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, -1.127271462664226e-05, 1, 0],
      [0, 0, 0, -2.168256415302494e-06, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, -1.470812982518055e-07, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [4.106973432893721, 0.0837579222787789, 4.087862515633204, 0.003258023951126177, 0.9544821830094157, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [14.11075145421835, 0.1296943777220876, 14.05872302828278, 0.01338829264042474, 0.9078841322957031, 0],
      [0, 0, 0, -1.401955747937222e-06, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [20.45496608009987, 1.02902873293605, 20.36538545022234, 0.01493243367754005, 0.9027419431126966, 0],
      [0, 1.399588068053353, 0, -0.001464396034913662, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, -7.717960819775271e-06, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [20.55602387476776, 0.228153246935258, 20.18257552588859, 0.01003676396826236, 0.9201985251667341, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [20.55602387476776, 0.228153246935258, 20.1825755258883, 0.01003675948773619, 0.920198542919369, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [14.24043411784638, 0.8098752083021072, 14.25358803525765, 0.007970007652421174, 0.9288634418318688, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, -7.647436724766976e-06, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, 0, 1, 0],
      [0, 0, 0, -8.179636239447063e-06, 1, 0]
      ]
    },
   "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 ration 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"]
    ]
  },
 "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":"spond@temple.edu",
   "info":"FEL (Fixed Effects Likelihood)\n    estimates site-wise synonymous (&alpha;) and non-synonymous (&beta;) 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.\n    ",
   "requirements":"in-frame codon alignment and a phylogenetic tree",
   "version":"2.1"
  },
 "branch attributes":{
   "0":{
     "Node20":{
       "Global MG94xREV":0.001634412620939209,
       "Nucleotide GTR":0.001684521619549293
      },
     "Node38":{
       "Global MG94xREV":0.001735516186079463,
       "Nucleotide GTR":0.00168484920326581
      },
     "Node4":{
       "Global MG94xREV":0.001634082124264937,
       "Nucleotide GTR":0.001683801387489096
      },
     "REFERENCE":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"REFERENCE"
      },
     "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021"
      },
     "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{
       "Global MG94xREV":0.001732287231356377,
       "Nucleotide GTR":0.001682745450340891,
       "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021"
      },
     "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021"
      },
     "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{
       "Global MG94xREV":0.001731614563238503,
       "Nucleotide GTR":0.00168274558227101,
       "original name":"epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021"
      },
     "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":{
       "Global MG94xREV":0.001735723694712937,
       "Nucleotide GTR":0.001684401404203384,
       "original name":"epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021"
      },
     "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{
       "Global MG94xREV":0.001732400229866267,
       "Nucleotide GTR":0.00168406792173386,
       "original name":"epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021"
      },
     "epi_isl_1543980_hCoV_19_Singapore_490_2021":{
       "Global MG94xREV":0.001734572377168157,
       "Nucleotide GTR":0.001684975469042935,
       "original name":"epi_isl_1543980/hCoV-19/Singapore/490/2021"
      },
     "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":{
       "Global MG94xREV":0.00173556721774995,
       "Nucleotide GTR":0.001684401583391051,
       "original name":"epi_isl_1544068/hCoV-19/India/MH-NCCS-RT231527/2021"
      },
     "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":{
       "Global MG94xREV":0.001732287295543277,
       "Nucleotide GTR":0.001682745512695379,
       "original name":"epi_isl_1573247/hCoV-19/Germany/un-RKI-I-068985/2021"
      },
     "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021"
      },
     "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":{
       "Global MG94xREV":0.001733756934810247,
       "Nucleotide GTR":0.001684431017860219,
       "original name":"epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021"
      },
     "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":{
       "Global MG94xREV":0.001733765377790725,
       "Nucleotide GTR":0.001684439221071522,
       "original name":"epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021"
      },
     "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"epi_isl_1615709/hCoV-19/England/CAMC-14E792B/2021"
      },
     "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":{
       "Global MG94xREV":0.001736016204276856,
       "Nucleotide GTR":0.00168443927661716,
       "original name":"epi_isl_1632256/hCoV-19/England/RAND-14E1D70/2021"
      },
     "epi_isl_1652105_hCoV_19_Singapore_561_2021":{
       "Global MG94xREV":0.001733699177045456,
       "Nucleotide GTR":0.001685171120971631,
       "original name":"epi_isl_1652105/hCoV-19/Singapore/561/2021"
      },
     "epi_isl_1652118_hCoV_19_Singapore_575_2021":{
       "Global MG94xREV":0.001733317358386759,
       "Nucleotide GTR":0.001684401899924961,
       "original name":"epi_isl_1652118/hCoV-19/Singapore/575/2021"
      },
     "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":{
       "Global MG94xREV":0.01050948252153795,
       "Nucleotide GTR":0.01020457779555702,
       "original name":"gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human"
      },
     "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.02683667587594947,
       "Nucleotide GTR":0.02592331511084145,
       "original name":"gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human"
      },
     "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.005257318397498607,
       "Nucleotide GTR":0.005093980037543817,
       "original name":"gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human"
      },
     "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.003479916225811642,
       "Nucleotide GTR":0.003379296026417724,
       "original name":"gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_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":{
       "Global MG94xREV":0.00346484907456443,
       "Nucleotide GTR":0.003372774424630234,
       "original name":"gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human"
      },
     "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.003473329356219227,
       "Nucleotide GTR":0.003374190595560375,
       "original name":"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_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.005214237519132295,
       "Nucleotide GTR":0.00505933790460295,
       "original name":"gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human"
      },
     "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":{
       "Global MG94xREV":0.003464011570187254,
       "Nucleotide GTR":0.003373764235314068,
       "original name":"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"
      },
     "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":{
       "Global MG94xREV":0.005236219940276191,
       "Nucleotide GTR":0.005068409188375663,
       "original name":"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"
      },
     "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.003464842731605314,
       "Nucleotide GTR":0.003372774424770855,
       "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"
      },
     "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.001735902734225727,
       "Nucleotide GTR":0.001686266012390882,
       "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"
      },
     "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":{
       "Global MG94xREV":0.003480097455920979,
       "Nucleotide GTR":0.003374436490976879,
       "original name":"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_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":{
       "Global MG94xREV":0.003472571057360136,
       "Nucleotide GTR":0.003376034743011948,
       "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"
      },
     "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":{
       "Global MG94xREV":0.003474988473611597,
       "Nucleotide GTR":0.003374190741831846,
       "original name":"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_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":{
       "Global MG94xREV":0.003471294890480852,
       "Nucleotide GTR":0.003376937492543959,
       "original name":"gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human"
      }
    },
   "attributes":{
     "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":"fel.filter.default"
    }
  },
 "fits":{
   "Global MG94xREV":{
     "AIC-c":2512.96200112621,
     "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":-1205.05897637469,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *background*":        [
[0.4929148115423557, 1]
        ],
       "non-synonymous/synonymous rate ratio for *test*":        [
[24.31954781803373, 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":{
   "FEL analysis":{
     "order":2,
     "timer":4
    },
   "Model fitting":{
     "order":1,
     "timer":6
    },
   "Total time":{
     "order":0,
     "timer":10
    }
  }
}
author	iuc
date	Wed, 30 Mar 2022 00:18:55 +0000
parents	8741542f9bc8
children