Mercurial > repos > rdvelazquez > hyphy_gard

annotate test-data/meme-out1.json @ 0:e489b7f00db7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6da8a2296bb256e47852690cf2221a7c943d8adc\n'-dirty
author rdvelazquez
date Tue, 04 Dec 2018 10:45:05 -0500
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e489b7f00db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6da8a2296bb256e47852690cf2221a7c943d8adc\n'-dirty
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1 {
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2 "analysis":{
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3 "info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous\n (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if β+ > α at a site.\n The estimates aggregate information over a proportion of branches at a site,\n so the signal is derived from\n episodic diversification, which is a combination of strength of selection [effect size] and\n the proportion of the tree affected. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ",
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4 "version":"2.0.1",
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5 "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.",
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6 "authors":"Sergei L. Kosakovsky Pond, Steven Weaver",
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7 "contact":"spond@temple.edu",
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8 "requirements":"in-frame codon alignment and a phylogenetic tree"
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9 },
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10 "fits":{
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11 "Nucleotide GTR":{
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12 "Log Likelihood":-4394.17778442101,
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13 "estimated parameters":47,
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14 "AIC-c":8882.482274823486,
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15 "Equilibrium frequencies":[
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20 ],
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21 "Rate Distributions":{
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22 "Substitution rate from nucleotide A to nucleotide C":0.1602243049428088,
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23 "Substitution rate from nucleotide A to nucleotide G":1,
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24 "Substitution rate from nucleotide A to nucleotide T":0.1350661843114337,
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25 "Substitution rate from nucleotide C to nucleotide G":0.04669906431175039,
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26 "Substitution rate from nucleotide C to nucleotide T":1.290725939052547,
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27 "Substitution rate from nucleotide G to nucleotide T":0.1442807316736102
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28 },
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29 "display order":0
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30 },
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31 "Global MG94xREV":{
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32 "Log Likelihood":-4272.739394378317,
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33 "estimated parameters":54,
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34 "AIC-c":8653.980859587502,
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35 "Equilibrium frequencies":[
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98 "Rate Distributions":{
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99 "non-synonymous/synonymous rate ratio for *test*":[
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101 ]
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102 },
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103 "display order":1
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104 }
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105 },
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106 "timers":{
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107 "Total time":{
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108 "timer":816,
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109 "order":0
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110 },
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111 "Model fitting":{
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112 "timer":12,
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113 "order":1
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114 },
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115 "MEME analysis":{
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116 "timer":803,
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117 "order":2
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118 }
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119 },
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120 "tested":{
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121 "0":{
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122 "TREESPARROW_HENAN_1_2004":"test",
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123 "TREESPARROW_HENAN_3_2004":"test",
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124 "Node6":"test",
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125 "TREESPARROW_HENAN_4_2004":"test",
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126 "Node5":"test",
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127 "CHICKEN_HEBEI_326_2005":"test",
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128 "SWINE_ANHUI_1_2004":"test",
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129 "TREESPARROW_HENAN_2_2004":"test",
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130 "Node12":"test",
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131 "Node10":"test",
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132 "Node4":"test",
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133 "CHICKEN_HONGKONG_915_97":"test",
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134 "GOOSE_HONGKONG_W355_97":"test",
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135 "DUCK_HONGKONG_Y283_97":"test",
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136 "Node19":"test",
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137 "Node17":"test",
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138 "HONGKONG_1_97_98":"test",
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139 "Node16":"test",
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140 "HONGKONG_1_538_97":"test",
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141 "Node15":"test",
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142 "Node3":"test",
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143 "DUCK_GUANGZHOU_20_2005":"test",
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144 "GOOSE_SHANTOU_2216_2005":"test",
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145 "Node26":"test",
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146 "PEREGRINEFALCON_HK_D0028_2004":"test",
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147 "Node25":"test",
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148 "CK_HK_WF157_2003":"test",
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149 "Node24":"test",
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150 "Node2":"test",
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151 "HUMAN_VIETNAM_CL105_2005":"test",
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152 "DUCK_VIETNAM_376_2005":"test",
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153 "Node33":"test",
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154 "HUMAN_VIETNAM_3062_2004":"test",
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155 "Node32":"test",
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156 "MALLARD_VIETNAM_16_2003":"test",
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157 "Node31":"test",
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158 "Node1":"test",
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159 "CHICKEN_CK_160_2005":"test",
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160 "DUCK_VIETNAM_272_2005":"test"
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161 }
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162 },
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163 "input":{
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164 "file name":"/tmp/tmpv_gXOY/job_working_directory/002/2719/working/meme_input.fa",
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165 "number of sequences":21,
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166 "number of sites":566,
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167 "partition count":1,
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168 "trees":{
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169 "0":"(((((((TREESPARROW_HENAN_1_2004:0.0111334,TREESPARROW_HENAN_3_2004:0.00619375)Node6:0.000995666,TREESPARROW_HENAN_4_2004:0.00435165)Node5:0.00226776,(CHICKEN_HEBEI_326_2005:0.0210089,(SWINE_ANHUI_1_2004:0.00770239,TREESPARROW_HENAN_2_2004:0.00906278)Node12:0.00209522)Node10:0.00388724)Node4:0.00340492,(((CHICKEN_HONGKONG_915_97:-1,(GOOSE_HONGKONG_W355_97:-1,DUCK_HONGKONG_Y283_97:0.00279842)Node19:0.00289977)Node17:0.00130638,HONGKONG_1_97_98:0.00384493)Node16:0.000182536,HONGKONG_1_538_97:-1)Node15:0.0209617)Node3:0.00313061,(((DUCK_GUANGZHOU_20_2005:0.00629939,GOOSE_SHANTOU_2216_2005:0.00620784)Node26:0.00253061,PEREGRINEFALCON_HK_D0028_2004:0.0036083)Node25:0.0032889,CK_HK_WF157_2003:0.0066313)Node24:0.0046553)Node2:0.0116809,(((HUMAN_VIETNAM_CL105_2005:0.00652152,DUCK_VIETNAM_376_2005:0.00787762)Node33:0.00196789,HUMAN_VIETNAM_3062_2004:0.0016414)Node32:0.000312551,MALLARD_VIETNAM_16_2003:0.00324422)Node31:0.000412598)Node1:0.000340091,CHICKEN_CK_160_2005:0.00616834,DUCK_VIETNAM_272_2005:0.0094653)"
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170 }
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171 },
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172 "data partitions":{
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173 "0":{
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174 "name":"meme.filter.default",
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175 "coverage":[
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177 ]
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178 }
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179 },
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180 "branch attributes":{
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181 "0":{
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182 "TREESPARROW_HENAN_1_2004":{
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183 "original name":"TREESPARROW_HENAN_1_2004",
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184 "Nucleotide GTR":0.01066479252384179,
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185 "Global MG94xREV":0.01076673590455662,
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186 "EBF site 3 (partition 1)":0.9456096051294662,
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187 "EBF site 8 (partition 1)":1162.743096991633,
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188 "EBF site 9 (partition 1)":1,
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189 "EBF site 10 (partition 1)":218.8691185742497,
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190 "EBF site 11 (partition 1)":127.9229379574454,
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191 "EBF site 12 (partition 1)":1,
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192 "EBF site 16 (partition 1)":0.9451095622554209,
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195 "EBF site 21 (partition 1)":176.9630563981623,
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196 "EBF site 26 (partition 1)":408.9192237736214,
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208 "EBF site 52 (partition 1)":1,
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212 "EBF site 60 (partition 1)":0.9841498071715201,
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1238 "original name":"HUMAN_VIETNAM_3062_2004",
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1239 "Nucleotide GTR":0.001781425550267506,
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1434 "EBF site 527 (partition 1)":0.9820906925833945,
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1435 "EBF site 529 (partition 1)":0.9910320967381681,
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1444 "EBF site 558 (partition 1)":0.9762431532734251,
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1447 },
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1448 "GOOSE_HONGKONG_W355_97":{
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rdvelazquez
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1449 "original name":"GOOSE_HONGKONG_W355_97",
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1450 "Nucleotide GTR":0,
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1451 "Global MG94xREV":0,
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1452 "EBF site 3 (partition 1)":1.000000004454476,
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1453 "EBF site 8 (partition 1)":0.9999999964832573,
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1455 "EBF site 10 (partition 1)":0.9999999977938284,
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1456 "EBF site 11 (partition 1)":0.9999999997642667,
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1457 "EBF site 12 (partition 1)":1,
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1458 "EBF site 16 (partition 1)":0.9999999982866217,
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1461 "EBF site 21 (partition 1)":0.9999999977979862,
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1462 "EBF site 26 (partition 1)":0.9999999951179953,
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1463 "EBF site 27 (partition 1)":1,
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1465 "EBF site 32 (partition 1)":1,
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1466 "EBF site 33 (partition 1)":1,
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1467 "EBF site 34 (partition 1)":1,
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1468 "EBF site 37 (partition 1)":1,
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1469 "EBF site 39 (partition 1)":1,
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1470 "EBF site 45 (partition 1)":1,
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1471 "EBF site 49 (partition 1)":1,
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1473 "EBF site 51 (partition 1)":1.000000003389824,
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1474 "EBF site 52 (partition 1)":1,
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1475 "EBF site 54 (partition 1)":1,
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1476 "EBF site 58 (partition 1)":1,
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1477 "EBF site 59 (partition 1)":1,
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1521 "EBF site 156 (partition 1)":1.000000004606383,
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1522 "EBF site 157 (partition 1)":0.999999996366886,
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1525 "EBF site 171 (partition 1)":1.000000004708058,
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1526 "EBF site 172 (partition 1)":1.000000002345886,
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1530 "EBF site 179 (partition 1)":0.9999999967984248,
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1537 "EBF site 200 (partition 1)":1.000000001581357,
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1547 "EBF site 221 (partition 1)":1,
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1550 "EBF site 226 (partition 1)":1,
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1551 "EBF site 228 (partition 1)":1.000000000105371,
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1554 "EBF site 233 (partition 1)":0.999999995100103,
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1555 "EBF site 235 (partition 1)":1,
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1556 "EBF site 236 (partition 1)":1,
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rdvelazquez
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1660 "original name":"DUCK_HONGKONG_Y283_97",
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1843 "EBF site 489 (partition 1)":0.9999999979293545,
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1845 "EBF site 494 (partition 1)":1,
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1846 "EBF site 499 (partition 1)":1,
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1847 "EBF site 500 (partition 1)":1,
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1848 "EBF site 506 (partition 1)":1,
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1849 "EBF site 507 (partition 1)":1,
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1850 "EBF site 508 (partition 1)":1,
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1851 "EBF site 509 (partition 1)":1,
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1854 "EBF site 515 (partition 1)":1,
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1856 "EBF site 527 (partition 1)":0.9999999985042536,
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1857 "EBF site 529 (partition 1)":1.000000002003295,
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1861 "EBF site 540 (partition 1)":1,
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1869 },
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rdvelazquez
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1870 "DUCK_VIETNAM_376_2005":{
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rdvelazquez
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1871 "original name":"DUCK_VIETNAM_376_2005",
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rdvelazquez
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1872 "Nucleotide GTR":0.008353464800246744,
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rdvelazquez
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1873 "Global MG94xREV":0.008507588898480372,
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1900 "EBF site 60 (partition 1)":0.9874069141126161,
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1918 "EBF site 99 (partition 1)":0.9222243378497063,
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1924 "EBF site 110 (partition 1)":0.9173232424122557,
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1926 "EBF site 113 (partition 1)":0.5760273516290358,
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1932 "EBF site 140 (partition 1)":1,
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1933 "EBF site 142 (partition 1)":0.8768947818177953,
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1951 "EBF site 178 (partition 1)":0.4028211720090112,
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1952 "EBF site 179 (partition 1)":145.750623030693,
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1953 "EBF site 181 (partition 1)":1,
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1954 "EBF site 185 (partition 1)":0.04589168935206885,
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1955 "EBF site 191 (partition 1)":0.7977552943260235,
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1956 "EBF site 195 (partition 1)":1,
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1957 "EBF site 196 (partition 1)":1,
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1958 "EBF site 197 (partition 1)":1,
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1959 "EBF site 200 (partition 1)":0.9565341582444904,
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1960 "EBF site 201 (partition 1)":0.916222865107566,
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rdvelazquez
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1961 "EBF site 204 (partition 1)":0.7248982098008665,
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rdvelazquez
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1962 "EBF site 206 (partition 1)":1,
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1963 "EBF site 209 (partition 1)":1,
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1964 "EBF site 211 (partition 1)":0.9140385369958551,
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1965 "EBF site 212 (partition 1)":1,
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rdvelazquez
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1966 "EBF site 213 (partition 1)":1,
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rdvelazquez
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1967 "EBF site 214 (partition 1)":0.3752557925768049,
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1968 "EBF site 217 (partition 1)":1,
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1969 "EBF site 221 (partition 1)":1,
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rdvelazquez
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1970 "EBF site 222 (partition 1)":1,
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1971 "EBF site 224 (partition 1)":1,
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rdvelazquez
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1972 "EBF site 226 (partition 1)":1,
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rdvelazquez
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1973 "EBF site 228 (partition 1)":0.9007558657573438,
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1974 "EBF site 230 (partition 1)":1,
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1975 "EBF site 231 (partition 1)":1,
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1976 "EBF site 233 (partition 1)":0.9579320644469356,
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rdvelazquez
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1977 "EBF site 235 (partition 1)":322.7347759782938,
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rdvelazquez
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1978 "EBF site 236 (partition 1)":1,
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rdvelazquez
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1979 "EBF site 237 (partition 1)":1,
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rdvelazquez
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1980 "EBF site 240 (partition 1)":1,
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rdvelazquez
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1981 "EBF site 241 (partition 1)":1,
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rdvelazquez
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1982 "EBF site 242 (partition 1)":3.593458681512879,
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1983 "EBF site 250 (partition 1)":1,
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1984 "EBF site 253 (partition 1)":1,
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rdvelazquez
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1985 "EBF site 254 (partition 1)":1,
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rdvelazquez
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1986 "EBF site 256 (partition 1)":1,
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rdvelazquez
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1987 "EBF site 258 (partition 1)":0.9575860982877624,
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rdvelazquez
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1988 "EBF site 265 (partition 1)":1,
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rdvelazquez
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1989 "EBF site 268 (partition 1)":1,
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rdvelazquez
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1990 "EBF site 271 (partition 1)":1,
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rdvelazquez
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1991 "EBF site 278 (partition 1)":1,
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rdvelazquez
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1992 "EBF site 279 (partition 1)":1,
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rdvelazquez
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1993 "EBF site 282 (partition 1)":1,
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rdvelazquez
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1994 "EBF site 283 (partition 1)":1,
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rdvelazquez
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1995 "EBF site 288 (partition 1)":1,
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rdvelazquez
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1996 "EBF site 291 (partition 1)":1,
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rdvelazquez
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1997 "EBF site 293 (partition 1)":1,
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rdvelazquez
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1998 "EBF site 296 (partition 1)":1,
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rdvelazquez
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1999 "EBF site 298 (partition 1)":0.3723346163223445,
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rdvelazquez
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2000 "EBF site 302 (partition 1)":1,
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rdvelazquez
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2001 "EBF site 304 (partition 1)":1,
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rdvelazquez
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2002 "EBF site 306 (partition 1)":1,
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rdvelazquez
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2003 "EBF site 309 (partition 1)":1,
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rdvelazquez
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2004 "EBF site 311 (partition 1)":1,
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rdvelazquez
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2005 "EBF site 312 (partition 1)":1,
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rdvelazquez
parents:
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2006 "EBF site 315 (partition 1)":0.9573908390602411,
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rdvelazquez
parents:
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2007 "EBF site 317 (partition 1)":1,
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rdvelazquez
parents:
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2008 "EBF site 327 (partition 1)":1,
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rdvelazquez
parents:
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2009 "EBF site 328 (partition 1)":1,
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rdvelazquez
parents:
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2010 "EBF site 329 (partition 1)":1,
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rdvelazquez
parents:
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2011 "EBF site 331 (partition 1)":1,
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rdvelazquez
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2012 "EBF site 332 (partition 1)":1,
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rdvelazquez
parents:
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2013 "EBF site 336 (partition 1)":0.07737790620602035,
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rdvelazquez
parents:
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2014 "EBF site 338 (partition 1)":0.6815814401903888,
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rdvelazquez
parents:
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2015 "EBF site 339 (partition 1)":1,
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rdvelazquez
parents:
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2016 "EBF site 341 (partition 1)":0.8241912078366742,
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rdvelazquez
parents:
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2017 "EBF site 342 (partition 1)":0.95742755918444,
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rdvelazquez
parents:
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2018 "EBF site 344 (partition 1)":1,
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rdvelazquez
parents:
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2019 "EBF site 348 (partition 1)":1,
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rdvelazquez
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2020 "EBF site 351 (partition 1)":1,
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rdvelazquez
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2021 "EBF site 353 (partition 1)":1,
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2022 "EBF site 354 (partition 1)":1,
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2023 "EBF site 357 (partition 1)":1,
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rdvelazquez
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2024 "EBF site 358 (partition 1)":1,
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rdvelazquez
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2025 "EBF site 361 (partition 1)":1,
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rdvelazquez
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2026 "EBF site 362 (partition 1)":1,
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rdvelazquez
parents:
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2027 "EBF site 369 (partition 1)":1,
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rdvelazquez
parents:
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2028 "EBF site 375 (partition 1)":1,
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rdvelazquez
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2029 "EBF site 377 (partition 1)":1,
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2080 },
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2082 "original name":"MALLARD_VIETNAM_16_2003",
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2504 "original name":"DUCK_GUANGZHOU_20_2005",
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2715 "original name":"CK_HK_WF157_2003",
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2926 "original name":"SWINE_ANHUI_1_2004",
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3346 },
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3347 "HONGKONG_1_97_98":{
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3348 "original name":"HONGKONG_1_97_98",
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3349 "Nucleotide GTR":0.004255948086831154,
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3558 "GOOSE_SHANTOU_2216_2005":{
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3559 "original name":"GOOSE_SHANTOU_2216_2005",
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3770 "original name":"TREESPARROW_HENAN_3_2004",
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3981 "original name":"PEREGRINEFALCON_HK_D0028_2004",
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3982 "Nucleotide GTR":0.003605869024912319,
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4191 "TREESPARROW_HENAN_2_2004":{
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4192 "original name":"TREESPARROW_HENAN_2_2004",
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4264 "EBF site 156 (partition 1)":0.9381216592668974,
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4523 "EBF site 278 (partition 1)":1,
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4524 "EBF site 279 (partition 1)":1,
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4525 "EBF site 282 (partition 1)":1,
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4526 "EBF site 283 (partition 1)":1,
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rdvelazquez
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5465 "EBF site 21 (partition 1)":0.9999999977979862,
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5525 "EBF site 156 (partition 1)":1.000000004606383,
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5526 "EBF site 157 (partition 1)":0.999999996366886,
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5529 "EBF site 171 (partition 1)":1.000000004708058,
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5530 "EBF site 172 (partition 1)":1.000000002345886,
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5541 "EBF site 200 (partition 1)":1.000000001581357,
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5542 "EBF site 201 (partition 1)":1,
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5543 "EBF site 204 (partition 1)":1,
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7342 },
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7343 "Node32":{
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rdvelazquez
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7569 "EBF site 32 (partition 1)":0.9846814907721615,
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7576 "EBF site 50 (partition 1)":1,
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7577 "EBF site 51 (partition 1)":0.9882731269808147,
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7578 "EBF site 52 (partition 1)":1,
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9230 }
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9231 }
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9232 },
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9233 "MLE":{
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9234 "headers":[
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9235 ["alpha;", "Synonymous substitution rate at a site"],
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9236 ["&beta;<sup>-</sup>", "Non-synonymous substitution rate at a site for the negative/neutral evolution component"],
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9237 ["p<sup>-</sup>", "Mixture distribution weight allocated to &beta;<sup>-</sup>; loosely -- the proportion of the tree evolving neutrally or under negative selection"],
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9238 ["&beta;<sup>+</sup>", "Non-synonymous substitution rate at a site for the positive/neutral evolution component"],
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diff changeset
9239 ["p<sup>+</sup>", "Mixture distribution weight allocated to &beta;<sup>+</sup>; loosely -- the proportion of the tree evolving neutrally or under positive selection"],
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diff changeset
9240 ["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p<sup>+</sup> &gt; 0 <emph>and<emph> &beta;<sup>+</sup> &gt; &alpha;"],
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diff changeset
9241 ["p-value", "Asymptotic p-value for episodic diversification, i.e., p<sup>+</sup> &gt; 0 <emph>and<emph> &beta;<sup>+</sup> &gt; &alpha;"],
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9242 ["# branches under selection", "The (very approximate and rough) estimate of how many branches may have been under selection at this site, i.e., had an empirical Bayes factor of 100 or more for the &beta;<sup>+</sup> rate"],
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diff changeset
9243 ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
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9244 ],
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9245 "content":{
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9246 "0":[
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