Mercurial > repos > iuc > hyphy_summary

annotate test-data/summary/nsp8.RELAX.json @ 3:bd90215b7d15 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 ec5db8349483b2cd46f9da23abe6cefcf65bc714"
author iuc
date Sat, 03 Jul 2021 08:53:45 +0000
parents f304c108aa1f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
1 {
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iuc
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2 "Synonymous site-posteriors": [
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diff changeset
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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6 ],
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7 "analysis":0,
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8 "branch attributes":{
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9 "0":{
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10 "Node20":{
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iuc
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12 "Nucleotide GTR":0.001684521619549293,
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iuc
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diff changeset
13 "RELAX alternative":0.001888715982590274,
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14 "RELAX null":0.001729201145341893
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15 },
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16 "Node38":{
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17 "MG94xREV with separate rates for branch sets":0.001919664136946674,
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18 "Nucleotide GTR":0.00168484920326581,
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19 "RELAX alternative":0.001886373803275281,
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20 "RELAX null":0.001757668602191916
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21 },
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22 "Node4":{
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24 "Nucleotide GTR":0.001683801387489096,
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25 "RELAX alternative":0.001736927843216757,
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26 "RELAX null":0.001719649158870973
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27 },
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28 "REFERENCE":{
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29 "MG94xREV with separate rates for branch sets":0,
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30 "Nucleotide GTR":0,
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31 "RELAX alternative":0,
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32 "RELAX null":0,
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33 "original name":"REFERENCE"
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34 },
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35 "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{
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36 "MG94xREV with separate rates for branch sets":0,
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37 "Nucleotide GTR":0,
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38 "RELAX alternative":0,
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39 "RELAX null":0,
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40 "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021"
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41 },
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42 "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{
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44 "Nucleotide GTR":0.001682745450340891,
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45 "RELAX alternative":0.001737560358174388,
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46 "RELAX null":0.001737701430364698,
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47 "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021"
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48 },
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49 "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{
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51 "Nucleotide GTR":0,
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54 "original name":"epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021"
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55 },
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56 "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{
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58 "Nucleotide GTR":0.00168274558227101,
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59 "RELAX alternative":0.001722861223551411,
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60 "RELAX null":0.001721507731204673,
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61 "original name":"epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021"
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62 },
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63 "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":{
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65 "Nucleotide GTR":0.001684401404203384,
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66 "RELAX alternative":0.00172720734036594,
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67 "RELAX null":0.001726404293760867,
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68 "original name":"epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021"
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70 "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{
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72 "Nucleotide GTR":0.00168406792173386,
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iuc
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iuc
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diff changeset
75 "original name":"epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021"
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iuc
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77 "epi_isl_1543980_hCoV_19_Singapore_490_2021":{
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iuc
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79 "Nucleotide GTR":0.001684975469042935,
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iuc
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iuc
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iuc
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diff changeset
82 "original name":"epi_isl_1543980/hCoV-19/Singapore/490/2021"
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83 },
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iuc
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84 "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":{
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iuc
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86 "Nucleotide GTR":0.001684401583391051,
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iuc
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iuc
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88 "RELAX null":0.001742131810362083,
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iuc
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89 "original name":"epi_isl_1544068/hCoV-19/India/MH-NCCS-RT231527/2021"
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iuc
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91 "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":{
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iuc
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93 "Nucleotide GTR":0.001682745512695379,
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iuc
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iuc
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95 "RELAX null":0.001737700138099048,
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iuc
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96 "original name":"epi_isl_1573247/hCoV-19/Germany/un-RKI-I-068985/2021"
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iuc
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97 },
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iuc
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98 "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":{
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iuc
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100 "Nucleotide GTR":0,
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iuc
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101 "RELAX alternative":0,
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iuc
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102 "RELAX null":0,
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iuc
parents:
diff changeset
103 "original name":"epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021"
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iuc
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104 },
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iuc
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105 "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":{
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iuc
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107 "Nucleotide GTR":0.001684431017860219,
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iuc
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108 "RELAX alternative":0.001731585452394539,
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iuc
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109 "RELAX null":0.001730940698634506,
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iuc
parents:
diff changeset
110 "original name":"epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021"
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iuc
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111 },
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iuc
parents:
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112 "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":{
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iuc
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113 "MG94xREV with separate rates for branch sets":0.001730283048611941,
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iuc
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114 "Nucleotide GTR":0.001684439221071522,
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iuc
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115 "RELAX alternative":0.001731571223917744,
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iuc
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116 "RELAX null":0.001730939668085807,
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iuc
parents:
diff changeset
117 "original name":"epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021"
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iuc
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118 },
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iuc
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diff changeset
119 "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":{
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120 "MG94xREV with separate rates for branch sets":0,
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iuc
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121 "Nucleotide GTR":0,
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iuc
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122 "RELAX alternative":0,
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iuc
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123 "RELAX null":0,
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iuc
parents:
diff changeset
124 "original name":"epi_isl_1615709/hCoV-19/England/CAMC-14E792B/2021"
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iuc
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125 },
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iuc
parents:
diff changeset
126 "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":{
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iuc
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127 "MG94xREV with separate rates for branch sets":0.001732590464662458,
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iuc
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128 "Nucleotide GTR":0.00168443927661716,
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iuc
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129 "RELAX alternative":0.001742601811734028,
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iuc
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130 "RELAX null":0.00174213227832234,
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iuc
parents:
diff changeset
131 "original name":"epi_isl_1632256/hCoV-19/England/RAND-14E1D70/2021"
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iuc
parents:
diff changeset
132 },
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iuc
parents:
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133 "epi_isl_1652105_hCoV_19_Singapore_561_2021":{
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iuc
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134 "MG94xREV with separate rates for branch sets":0.001730912430514071,
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iuc
parents:
diff changeset
135 "Nucleotide GTR":0.001685171120971631,
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iuc
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136 "RELAX alternative":0.001729942855612116,
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iuc
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137 "RELAX null":0.001729323731291246,
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iuc
parents:
diff changeset
138 "original name":"epi_isl_1652105/hCoV-19/Singapore/561/2021"
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iuc
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139 },
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iuc
parents:
diff changeset
140 "epi_isl_1652118_hCoV_19_Singapore_575_2021":{
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141 "MG94xREV with separate rates for branch sets":0.00173012682067509,
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iuc
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diff changeset
142 "Nucleotide GTR":0.001684401899924961,
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iuc
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143 "RELAX alternative":0.001728421813161176,
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iuc
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144 "RELAX null":0.001727458069395059,
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iuc
parents:
diff changeset
145 "original name":"epi_isl_1652118/hCoV-19/Singapore/575/2021"
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iuc
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146 },
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iuc
parents:
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147 "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":{
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iuc
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148 "MG94xREV with separate rates for branch sets":0.01048097601700974,
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iuc
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diff changeset
149 "Nucleotide GTR":0.01020457779555702,
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iuc
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150 "RELAX alternative":0.01047086585093888,
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iuc
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151 "RELAX null":0.01046479928106623,
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iuc
parents:
diff changeset
152 "original name":"gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human"
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iuc
parents:
diff changeset
153 },
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iuc
parents:
diff changeset
154 "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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iuc
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155 "MG94xREV with separate rates for branch sets":0.02680857528731593,
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iuc
parents:
diff changeset
156 "Nucleotide GTR":0.02592331511084145,
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iuc
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159 "original name":"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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iuc
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161 "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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166 "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"
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168 "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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173 "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"
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175 "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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182 "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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189 "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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194 "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"
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196 "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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201 "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"
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203 "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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iuc
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iuc
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208 "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"
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209 },
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iuc
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210 "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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212 "Nucleotide GTR":0.003372774424770855,
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iuc
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214 "RELAX null":0.003499034126859038,
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iuc
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215 "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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216 },
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217 "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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219 "Nucleotide GTR":0.001686266012390882,
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222 "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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223 },
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224 "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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226 "Nucleotide GTR":0.003374436490976879,
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229 "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"
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230 },
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diff changeset
231 "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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diff changeset
232 "MG94xREV with separate rates for branch sets":0.003465962437529985,
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diff changeset
233 "Nucleotide GTR":0.003376034743011948,
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diff changeset
234 "RELAX alternative":0.003505853316276177,
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diff changeset
235 "RELAX null":0.00350745511719164,
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iuc
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diff changeset
236 "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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diff changeset
237 },
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iuc
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diff changeset
238 "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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iuc
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diff changeset
240 "Nucleotide GTR":0.003374190741831846,
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iuc
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diff changeset
242 "RELAX null":0.003508905377887805,
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iuc
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diff changeset
243 "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"
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diff changeset
244 },
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iuc
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diff changeset
245 "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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247 "Nucleotide GTR":0.003376937492543959,
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iuc
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249 "RELAX null":0.003506633016642548,
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iuc
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diff changeset
250 "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"
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diff changeset
251 }
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252 },
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iuc
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253 "attributes":{
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diff changeset
255 "attribute type":"branch length",
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256 "display order":1
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257 },
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258 "Nucleotide GTR":{
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259 "attribute type":"branch length",
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260 "display order":0
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261 },
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262 "RELAX alternative":{
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263 "attribute type":"branch length",
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266 "RELAX null":{
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267 "attribute type":"branch length",
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270 "original name":{
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271 "attribute type":"node label",
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273 }
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274 }
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275 },
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276 "data partitions":{
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277 "0":{
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278 "coverage": [
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diff changeset
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281 "name":"relax.filter.default"
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282 }
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284 "fits":{
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diff changeset
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iuc
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iuc
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341 [0.02433965804833868],
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iuc
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iuc
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iuc
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345 [0.01755532734880559],
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iuc
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iuc
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iuc
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diff changeset
348 [0.02371882618448924]
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iuc
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diff changeset
349 ],
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iuc
parents:
diff changeset
350 "Log Likelihood":-1204.057620165384,
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iuc
parents:
diff changeset
351 "Rate Distributions":{
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iuc
parents:
diff changeset
352 "non-synonymous/synonymous rate ratio for *Reference*": [
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iuc
parents:
diff changeset
353 [0, 1]
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iuc
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diff changeset
354 ],
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iuc
parents:
diff changeset
355 "non-synonymous/synonymous rate ratio for *Test*": [
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iuc
parents:
diff changeset
356 [21.18256670135096, 1]
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iuc
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diff changeset
357 ],
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iuc
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diff changeset
358 "non-synonymous/synonymous rate ratio for *Unclassified*": [
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iuc
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diff changeset
359 [0.5156677179593993, 1]
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iuc
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diff changeset
360 ]
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iuc
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diff changeset
361 },
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iuc
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diff changeset
362 "display order":1,
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iuc
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diff changeset
363 "estimated parameters":52
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diff changeset
364 },
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iuc
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diff changeset
365 "Nucleotide GTR":{
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iuc
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diff changeset
366 "AIC-c":2633.0046471406,
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iuc
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diff changeset
367 "Equilibrium frequencies": [
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diff changeset
368 [0.3251262626262627],
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diff changeset
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iuc
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diff changeset
371 [0.2922979797979798]
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iuc
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diff changeset
372 ],
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iuc
parents:
diff changeset
373 "Log Likelihood":-1247.247280799152,
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iuc
parents:
diff changeset
374 "Rate Distributions":{
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iuc
parents:
diff changeset
375 "Substitution rate from nucleotide A to nucleotide C":0,
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iuc
parents:
diff changeset
376 "Substitution rate from nucleotide A to nucleotide G":1,
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iuc
parents:
diff changeset
377 "Substitution rate from nucleotide A to nucleotide T":0.3101631549852981,
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iuc
parents:
diff changeset
378 "Substitution rate from nucleotide C to nucleotide G":1.129990583516242,
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iuc
parents:
diff changeset
379 "Substitution rate from nucleotide C to nucleotide T":2.723444388603395,
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iuc
parents:
diff changeset
380 "Substitution rate from nucleotide G to nucleotide T":1.720896006888861
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iuc
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diff changeset
381 },
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iuc
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diff changeset
382 "display order":0,
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iuc
parents:
diff changeset
383 "estimated parameters":69
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iuc
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diff changeset
384 },
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iuc
parents:
diff changeset
385 "RELAX alternative":{
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iuc
parents:
diff changeset
386 "AIC-c":2539.023758734034,
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iuc
parents:
diff changeset
387 "Log Likelihood":-1203.827668840701,
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iuc
parents:
diff changeset
388 "Rate Distributions":{
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iuc
parents:
diff changeset
389 "Reference":{
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iuc
parents:
diff changeset
390 "0":{
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iuc
parents:
diff changeset
391 "omega":0,
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iuc
parents:
diff changeset
392 "proportion":0.3229316344832856
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iuc
parents:
diff changeset
393 },
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iuc
parents:
diff changeset
394 "1":{
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iuc
parents:
diff changeset
395 "omega":0,
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iuc
parents:
diff changeset
396 "proportion":0.6561871399951409
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iuc
parents:
diff changeset
397 },
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iuc
parents:
diff changeset
398 "2":{
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iuc
parents:
diff changeset
399 "omega":2.618905128891877,
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iuc
parents:
diff changeset
400 "proportion":0.02088122552157349
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iuc
parents:
diff changeset
401 }
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
402 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
403 "Synonymous site-to-site rates":{
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iuc
parents:
diff changeset
404 "0":{
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iuc
parents:
diff changeset
405 "proportion":0,
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iuc
parents:
diff changeset
406 "rate":0.8672539109745554
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iuc
parents:
diff changeset
407 },
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408 "1":{
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409 "proportion":1,
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411 },
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412 "2":{
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413 "proportion":0,
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414 "rate":1.04385559910209
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415 }
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416 },
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417 "Test":{
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418 "0":{
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420 "proportion":0.3229316344832856
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421 },
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422 "1":{
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423 "omega":0,
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424 "proportion":0.6561871399951409
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425 },
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426 "2":{
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427 "omega":887.8019782663979,
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428 "proportion":0.02088122552157349
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429 }
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430 }
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431 },
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432 "display order":2,
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433 "estimated parameters":65
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434 },
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435 "RELAX null":{
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436 "AIC-c":2540.205243445127,
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diff changeset
437 "Log Likelihood":-1205.43925064937,
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diff changeset
438 "Rate Distributions":{
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iuc
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439 "Reference":{
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iuc
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440 "0":{
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441 "omega":0.01761845549263694,
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442 "proportion":0.1028887690453239
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iuc
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diff changeset
443 },
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iuc
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444 "1":{
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445 "omega":0.1789488803563501,
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iuc
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446 "proportion":0.8141260406522884
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447 },
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iuc
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448 "2":{
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iuc
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449 "omega":5.480099329809248,
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iuc
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450 "proportion":0.08298519030238755
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iuc
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diff changeset
451 }
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iuc
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diff changeset
452 },
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iuc
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diff changeset
453 "Synonymous site-to-site rates":{
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iuc
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454 "0":{
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iuc
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455 "proportion":0,
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iuc
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diff changeset
456 "rate":0.8690455710978635
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iuc
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diff changeset
457 },
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iuc
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diff changeset
458 "1":{
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iuc
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459 "proportion":1,
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iuc
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diff changeset
460 "rate":1
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461 },
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iuc
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462 "2":{
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463 "proportion":0,
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iuc
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diff changeset
464 "rate":1.043145103957073
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iuc
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diff changeset
465 }
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iuc
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diff changeset
466 },
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iuc
parents:
diff changeset
467 "Test":{
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iuc
parents:
diff changeset
468 "0":{
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iuc
parents:
diff changeset
469 "omega":0.01761845549263694,
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iuc
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diff changeset
470 "proportion":0.1028887690453239
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iuc
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diff changeset
471 },
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iuc
parents:
diff changeset
472 "1":{
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iuc
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diff changeset
473 "omega":0.1789488803563501,
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iuc
parents:
diff changeset
474 "proportion":0.8141260406522884
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iuc
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diff changeset
475 },
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iuc
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diff changeset
476 "2":{
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iuc
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diff changeset
477 "omega":5.480099329809248,
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iuc
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diff changeset
478 "proportion":0.08298519030238755
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iuc
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diff changeset
479 }
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iuc
parents:
diff changeset
480 }
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iuc
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diff changeset
481 },
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iuc
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diff changeset
482 "display order":3,
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iuc
parents:
diff changeset
483 "estimated parameters":64
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iuc
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diff changeset
484 }
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iuc
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diff changeset
485 },
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iuc
parents:
diff changeset
486 "input":{
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iuc
parents:
diff changeset
487 "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas",
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iuc
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diff changeset
488 "number of sequences":32,
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iuc
parents:
diff changeset
489 "number of sites":198,
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iuc
parents:
diff changeset
490 "partition count":1,
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iuc
parents:
diff changeset
491 "trees":{
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iuc
parents:
diff changeset
492 "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)"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
493 }
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
494 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
495 "test results":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
496 "LRT":3.223163617336922,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
497 "p-value":0.07260318641568564,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
498 "relaxation or intensification parameter":7.051367447513434
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
499 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
500 "tested":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
501 "0":{
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iuc
parents:
diff changeset
502 "Node20":"Test",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
503 "Node38":"Reference",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
504 "Node4":"Test",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
505 "REFERENCE":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
506 "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
507 "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
508 "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
509 "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
510 "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
511 "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
512 "epi_isl_1543980_hCoV_19_Singapore_490_2021":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
513 "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
514 "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
515 "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
516 "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
517 "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
518 "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
519 "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
520 "epi_isl_1652105_hCoV_19_Singapore_561_2021":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
521 "epi_isl_1652118_hCoV_19_Singapore_575_2021":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
522 "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
523 "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
524 "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
525 "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
526 "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
527 "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
528 "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
529 "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":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
530 "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":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
531 "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
532 "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
533 "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":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
534 "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":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
535 "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":"Unclassified",
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
536 "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"Unclassified"
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
537 }
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
538 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
539 "timers":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
540 "Overall":{
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
541 "order":0,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
542 "timer":67
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
543 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
544 "Preliminary model fitting":{
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iuc
parents:
diff changeset
545 "order":1,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
546 "timer":5
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
547 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
548 "RELAX alternative model fitting":{
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iuc
parents:
diff changeset
549 "order":3,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
550 "timer":50
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
551 },
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
552 "RELAX null model fitting":{
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iuc
parents:
diff changeset
553 "order":4,
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
554 "timer":12
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
555 }
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
556 }
f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
557 }