Mercurial > repos > iuc > hyphy_fubar

annotate test-data/absrel-out1.json @ 1:0f108ee932ea 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 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
author iuc
date Wed, 21 Aug 2019 12:24:34 -0400
parents fe399429a5d2
children 47145f568cd6
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fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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1 {
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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2 "analysis":{
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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3 "info":"aBSREL (Adaptive branch-site random effects likelihood)\n uses an adaptive random effects branch-site model framework\n to test whether each branch has evolved under positive selection,\n using a procedure which infers an optimal number of rate categories per branch.",
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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4 "version":"2.0",
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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5 "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353",
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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6 "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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7 "contact":"spond@temple.edu",
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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8 "requirements":"in-frame codon alignment and a phylogenetic tree"
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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9 },
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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10 "input":{
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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11 "file name":"/tmp/tmpCAMqUO/job_working_directory/002/2602/working/absrel_input.fa",
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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12 "number of sequences":10,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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13 "number of sites":187,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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14 "partition count":1,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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15 "trees":{
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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16 "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.085099,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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17 }
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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18 },
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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19 "fits":{
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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20 "Nucleotide GTR":{
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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21 "Log Likelihood":-3531.96369518556,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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22 "estimated parameters":24,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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23 "AIC-c":7112.577796875186,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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24 "Equilibrium frequencies":[
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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29 ],
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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30 "Rate Distributions":{
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31 "Substitution rate from nucleotide A to nucleotide C":0.5474707834424497,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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32 "Substitution rate from nucleotide A to nucleotide G":1,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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33 "Substitution rate from nucleotide A to nucleotide T":0.2645731370379643,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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34 "Substitution rate from nucleotide C to nucleotide G":0.4867482826410435,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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35 "Substitution rate from nucleotide C to nucleotide T":1.018295973581558,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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36 "Substitution rate from nucleotide G to nucleotide T":0.3026112531229544
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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37 },
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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38 "display order":0
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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39 },
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40 "Baseline MG94xREV":{
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41 "Log Likelihood":-3450.669934819203,
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42 "estimated parameters":46,
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43 "AIC-c":6995.711784065174,
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44 "Equilibrium frequencies":[
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107 "Rate Distributions":{
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108 "Per-branch omega":{
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109 "Mean":666666667.6064719,
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110 "Median":1.103169534345197,
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111 "2.5%":0,
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112 "97.5%":10000000000
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113 }
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114 },
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115 "display order":1
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116 },
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117 "Full adaptive model":{
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118 "Log Likelihood":-3414.992415597899,
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119 "estimated parameters":60,
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120 "AIC-c":6954.031265689993,
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121 "Rate Distributions":{
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122 },
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123 "display order":2
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124 }
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125 },
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126 "timers":{
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127 "Overall":{
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128 "timer":98,
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129 "order":0
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130 },
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131 "Preliminary model fitting":{
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132 "timer":0,
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133 "order":1
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iuc
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134 },
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135 "Baseline model fitting":{
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136 "timer":1,
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137 "order":2
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138 },
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139 "Complexity analysis":{
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140 "timer":36,
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141 "order":3
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142 },
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143 "Full adaptive model fitting":{
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144 "timer":8,
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145 "order":4
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iuc
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146 },
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147 "Testing for selection":{
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iuc
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148 "timer":53,
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iuc
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149 "order":5
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iuc
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150 }
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151 },
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152 "test results":{
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153 "P-value threshold":0.05,
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154 "tested":16,
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155 "positive test results":3
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iuc
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156 },
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157 "tested":{
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iuc
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158 "0":{
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159 "Pig":"test",
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160 "Cow":"test",
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161 "Node3":"test",
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iuc
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162 "Horse":"test",
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iuc
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163 "Cat":"test",
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164 "Node2":"test",
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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165 "RhMonkey":"test",
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iuc
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166 "Baboon":"test",
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167 "Node9":"test",
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iuc
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168 "Human":"test",
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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169 "Chimp":"test",
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170 "Node12":"test",
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iuc
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171 "Node8":"test",
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iuc
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172 "Node1":"test",
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iuc
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173 "Rat":"test",
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iuc
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174 "Mouse":"test"
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iuc
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175 }
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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176 },
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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177 "data partitions":{
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iuc
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178 "0":{
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iuc
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179 "name":"absrel.filter.default",
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iuc
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180 "coverage":[
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iuc
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181 [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186]
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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182 ]
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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183 }
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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184 },
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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185 "branch attributes":{
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iuc
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186 "0":{
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iuc
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187 "Human":{
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iuc
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188 "original name":"Human",
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iuc
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189 "Nucleotide GTR":0,
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iuc
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190 "Baseline MG94xREV":0,
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iuc
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191 "Baseline MG94xREV omega ratio":1,
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iuc
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192 "Rate classes":1,
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iuc
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193 "Full adaptive model":0,
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iuc
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194 "Rate Distributions":[
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iuc
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195 [1, 1]
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iuc
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196 ],
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iuc
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197 "LRT":0,
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iuc
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198 "Uncorrected P-value":1,
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iuc
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199 "Corrected P-value":1
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iuc
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200 },
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iuc
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201 "Chimp":{
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iuc
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202 "original name":"Chimp",
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iuc
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diff changeset
203 "Nucleotide GTR":0.001818174796225333,
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iuc
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204 "Baseline MG94xREV":0.001839770270131542,
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iuc
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205 "Baseline MG94xREV omega ratio":10000000000,
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iuc
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206 "Rate classes":1,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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207 "Full adaptive model":0.001845806111200226,
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iuc
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208 "Rate Distributions":[
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iuc
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209 [10000000000, 1]
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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210 ],
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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211 "LRT":0.6362875427803374,
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iuc
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212 "Uncorrected P-value":0.303261123771571,
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iuc
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213 "Corrected P-value":1
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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214 },
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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215 "Baboon":{
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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216 "original name":"Baboon",
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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217 "Nucleotide GTR":0.001682034724848474,
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iuc
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218 "Baseline MG94xREV":0.001821072110941238,
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iuc
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219 "Baseline MG94xREV omega ratio":0,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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220 "Rate classes":1,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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221 "Full adaptive model":0.001808294153407354,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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222 "Rate Distributions":[
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iuc
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223 [0, 1]
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iuc
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224 ],
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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225 "LRT":0,
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iuc
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226 "Uncorrected P-value":1,
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iuc
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227 "Corrected P-value":1
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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228 },
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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229 "RhMonkey":{
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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230 "original name":"RhMonkey",
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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231 "Nucleotide GTR":0.003775509884015639,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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232 "Baseline MG94xREV":0.003671340584166445,
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iuc
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233 "Baseline MG94xREV omega ratio":10000000000,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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234 "Rate classes":1,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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235 "Full adaptive model":0.003682180830540259,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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236 "Rate Distributions":[
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iuc
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237 [10000000000, 1]
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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238 ],
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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239 "LRT":1.200615147074132,
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iuc
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240 "Uncorrected P-value":0.2192326116145807,
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iuc
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241 "Corrected P-value":1
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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242 },
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iuc
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243 "Cow":{
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iuc
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244 "original name":"Cow",
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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245 "Nucleotide GTR":0.248257545271419,
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iuc
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246 "Baseline MG94xREV":0.2535517510207829,
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iuc
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247 "Baseline MG94xREV omega ratio":1.957039676836281,
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iuc
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248 "Rate classes":2,
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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249 "Full adaptive model":0.3959632497370367,
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iuc
parents:
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250 "Rate Distributions":[
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iuc
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251 [0, 0.5384412409742189],
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iuc
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252 [10.58123012791267, 0.4615587590257811]
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iuc
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253 ],
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iuc
parents:
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254 "LRT":24.50128746473001,
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iuc
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255 "Uncorrected P-value":1.583131814197891e-06,
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iuc
parents:
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256 "Corrected P-value":2.533010902716626e-05
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iuc
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257 },
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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258 "Pig":{
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iuc
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259 "original name":"Pig",
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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260 "Nucleotide GTR":0.1872143003439852,
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iuc
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261 "Baseline MG94xREV":0.1913752025483544,
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iuc
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diff changeset
262 "Baseline MG94xREV omega ratio":1.354835319497051,
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iuc
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diff changeset
263 "Rate classes":1,
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iuc
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diff changeset
264 "Full adaptive model":0.1823079562415392,
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iuc
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265 "Rate Distributions":[
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iuc
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diff changeset
266 [1.270031670375847, 1]
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iuc
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iuc
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268 "LRT":0.5083013304356427,
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iuc
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269 "Uncorrected P-value":0.3278475069550038,
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iuc
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diff changeset
270 "Corrected P-value":1
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iuc
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diff changeset
271 },
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iuc
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272 "Horse":{
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iuc
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diff changeset
273 "original name":"Horse",
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iuc
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274 "Nucleotide GTR":0.2092211101976542,
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iuc
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275 "Baseline MG94xREV":0.2093433205074538,
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iuc
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276 "Baseline MG94xREV omega ratio":1.262933703792719,
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iuc
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diff changeset
277 "Rate classes":2,
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iuc
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278 "Full adaptive model":0.2696870893488891,
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iuc
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279 "Rate Distributions":[
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iuc
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280 [0, 0.5494326491453121],
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iuc
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281 [4.447670371762946, 0.4505673508546879]
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iuc
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iuc
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283 "LRT":9.839972152766677,
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iuc
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284 "Uncorrected P-value":0.002531289908698275,
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iuc
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285 "Corrected P-value":0.03543805872177586
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iuc
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diff changeset
286 },
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iuc
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diff changeset
287 "Cat":{
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iuc
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diff changeset
288 "original name":"Cat",
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iuc
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diff changeset
289 "Nucleotide GTR":0.2662269345134692,
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iuc
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290 "Baseline MG94xREV":0.2773733494290757,
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iuc
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diff changeset
291 "Baseline MG94xREV omega ratio":1.619113019542315,
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iuc
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diff changeset
292 "Rate classes":2,
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iuc
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293 "Full adaptive model":0.3637840333790108,
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iuc
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294 "Rate Distributions":[
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iuc
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295 [0.3427137549260186, 0.5775012741005606],
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iuc
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diff changeset
296 [6.025097508634321, 0.4224987258994394]
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iuc
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297 ],
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iuc
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diff changeset
298 "LRT":13.05292728184577,
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iuc
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299 "Uncorrected P-value":0.000499814517576469,
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iuc
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diff changeset
300 "Corrected P-value":0.007497217763647035
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iuc
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diff changeset
301 },
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iuc
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diff changeset
302 "Mouse":{
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iuc
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diff changeset
303 "original name":"Mouse",
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iuc
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diff changeset
304 "Nucleotide GTR":0.1181551390736968,
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iuc
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diff changeset
305 "Baseline MG94xREV":0.1220127721537473,
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iuc
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diff changeset
306 "Baseline MG94xREV omega ratio":0.5307054960008202,
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iuc
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diff changeset
307 "Rate classes":1,
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iuc
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diff changeset
308 "Full adaptive model":0.1200052061883895,
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iuc
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309 "Rate Distributions":[
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iuc
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diff changeset
310 [0.5418818043457002, 1]
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iuc
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iuc
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diff changeset
312 "LRT":0,
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iuc
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313 "Uncorrected P-value":1,
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iuc
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diff changeset
314 "Corrected P-value":1
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iuc
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diff changeset
315 },
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iuc
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diff changeset
316 "Rat":{
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iuc
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diff changeset
317 "original name":"Rat",
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iuc
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diff changeset
318 "Nucleotide GTR":0.06673994656462794,
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iuc
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diff changeset
319 "Baseline MG94xREV":0.06546903135094065,
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iuc
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diff changeset
320 "Baseline MG94xREV omega ratio":1.103169534345197,
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iuc
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diff changeset
321 "Rate classes":1,
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iuc
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diff changeset
322 "Full adaptive model":0.06894368446818594,
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iuc
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diff changeset
323 "Rate Distributions":[
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iuc
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diff changeset
324 [1.162844601638596, 1]
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iuc
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diff changeset
325 ],
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iuc
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326 "LRT":0.04180897168953379,
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iuc
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327 "Uncorrected P-value":0.4613906175252571,
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iuc
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diff changeset
328 "Corrected P-value":1
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iuc
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diff changeset
329 },
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iuc
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diff changeset
330 "Node1":{
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iuc
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diff changeset
331 "Nucleotide GTR":0.2772613398768408,
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iuc
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diff changeset
332 "Baseline MG94xREV":0.2903229694372956,
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iuc
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333 "Baseline MG94xREV omega ratio":0.4389914526526448,
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iuc
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diff changeset
334 "Rate classes":2,
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iuc
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diff changeset
335 "Full adaptive model":0.3664538683295676,
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iuc
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diff changeset
336 "Rate Distributions":[
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iuc
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diff changeset
337 [0.1934444279004118, 0.7920338324503209],
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iuc
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diff changeset
338 [2.595458156723663, 0.2079661675496791]
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iuc
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339 ],
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iuc
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diff changeset
340 "LRT":1.095302853601424,
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iuc
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diff changeset
341 "Uncorrected P-value":0.232551772988317,
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iuc
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diff changeset
342 "Corrected P-value":1
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iuc
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diff changeset
343 },
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iuc
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diff changeset
344 "Node12":{
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iuc
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345 "Nucleotide GTR":0.01783922546179193,
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iuc
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diff changeset
346 "Baseline MG94xREV":0.01797212760838867,
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iuc
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diff changeset
347 "Baseline MG94xREV omega ratio":0.3712490894908597,
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iuc
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diff changeset
348 "Rate classes":1,
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iuc
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diff changeset
349 "Full adaptive model":0.01648897148329989,
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iuc
parents:
diff changeset
350 "Rate Distributions":[
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iuc
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diff changeset
351 [0.3341484726344874, 1]
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iuc
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diff changeset
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iuc
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diff changeset
353 "LRT":0,
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iuc
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354 "Uncorrected P-value":1,
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iuc
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diff changeset
355 "Corrected P-value":1
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iuc
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diff changeset
356 },
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iuc
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diff changeset
357 "Node2":{
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iuc
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diff changeset
358 "Nucleotide GTR":0.06619058539001231,
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iuc
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diff changeset
359 "Baseline MG94xREV":0.06580724801157116,
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iuc
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diff changeset
360 "Baseline MG94xREV omega ratio":0.6811307469311604,
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iuc
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diff changeset
361 "Rate classes":2,
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iuc
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diff changeset
362 "Full adaptive model":0.1259563484776556,
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iuc
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diff changeset
363 "Rate Distributions":[
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iuc
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364 [0, 0.902872882268449],
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iuc
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diff changeset
365 [33.80023214939837, 0.09712711773155103]
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iuc
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diff changeset
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iuc
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diff changeset
367 "LRT":7.670975764417562,
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iuc
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diff changeset
368 "Uncorrected P-value":0.007599562698001494,
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iuc
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diff changeset
369 "Corrected P-value":0.09119475237601793
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iuc
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diff changeset
370 },
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iuc
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diff changeset
371 "Node3":{
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iuc
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diff changeset
372 "Nucleotide GTR":0.09883236156840018,
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iuc
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diff changeset
373 "Baseline MG94xREV":0.102749851157051,
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iuc
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diff changeset
374 "Baseline MG94xREV omega ratio":1.47449378631578,
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iuc
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diff changeset
375 "Rate classes":2,
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iuc
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diff changeset
376 "Full adaptive model":0.1389308407753113,
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iuc
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diff changeset
377 "Rate Distributions":[
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iuc
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diff changeset
378 [0, 0.7024206790833775],
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iuc
parents:
diff changeset
379 [8.065310624699681, 0.2975793209166225]
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iuc
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diff changeset
380 ],
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iuc
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diff changeset
381 "LRT":6.598417720076213,
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iuc
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diff changeset
382 "Uncorrected P-value":0.0131150962965953,
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iuc
parents:
diff changeset
383 "Corrected P-value":0.1442660592625483
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iuc
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diff changeset
384 },
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iuc
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diff changeset
385 "Node8":{
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iuc
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diff changeset
386 "Nucleotide GTR":0.1061134663636472,
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iuc
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diff changeset
387 "Baseline MG94xREV":0.110140333084973,
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iuc
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diff changeset
388 "Baseline MG94xREV omega ratio":1.896243438714738,
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iuc
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diff changeset
389 "Rate classes":2,
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iuc
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diff changeset
390 "Full adaptive model":0.2165540926910564,
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iuc
parents:
diff changeset
391 "Rate Distributions":[
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iuc
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diff changeset
392 [1, 0.9077840705139004],
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iuc
parents:
diff changeset
393 [33.32075865076668, 0.09221592948609958]
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iuc
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diff changeset
394 ],
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iuc
parents:
diff changeset
395 "LRT":7.97288393366216,
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iuc
parents:
diff changeset
396 "Uncorrected P-value":0.006519360772582139,
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iuc
parents:
diff changeset
397 "Corrected P-value":0.08475169004356781
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iuc
parents:
diff changeset
398 },
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iuc
parents:
diff changeset
399 "Node9":{
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iuc
parents:
diff changeset
400 "Nucleotide GTR":0.02566719422260768,
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iuc
parents:
diff changeset
401 "Baseline MG94xREV":0.02590165433349057,
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iuc
parents:
diff changeset
402 "Baseline MG94xREV omega ratio":0.4071738826525522,
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iuc
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diff changeset
403 "Rate classes":1,
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iuc
parents:
diff changeset
404 "Full adaptive model":0.02766629863085238,
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iuc
parents:
diff changeset
405 "Rate Distributions":[
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iuc
parents:
diff changeset
406 [0.4488424899910019, 1]
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iuc
parents:
diff changeset
407 ],
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iuc
parents:
diff changeset
408 "LRT":0,
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iuc
parents:
diff changeset
409 "Uncorrected P-value":1,
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iuc
parents:
diff changeset
410 "Corrected P-value":1
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iuc
parents:
diff changeset
411 }
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iuc
parents:
diff changeset
412 },
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iuc
parents:
diff changeset
413 "attributes":{
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iuc
parents:
diff changeset
414 "original name":{
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iuc
parents:
diff changeset
415 "attribute type":"node label",
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iuc
parents:
diff changeset
416 "display order":-1
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iuc
parents:
diff changeset
417 },
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iuc
parents:
diff changeset
418 "Nucleotide GTR":{
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iuc
parents:
diff changeset
419 "attribute type":"branch length",
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iuc
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diff changeset
420 "display order":0
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iuc
parents:
diff changeset
421 },
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iuc
parents:
diff changeset
422 "Baseline MG94xREV":{
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iuc
parents:
diff changeset
423 "attribute type":"branch length",
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iuc
parents:
diff changeset
424 "display order":1
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
425 },
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iuc
parents:
diff changeset
426 "Baseline MG94xREV omega ratio":{
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iuc
parents:
diff changeset
427 "attribute type":"branch label",
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iuc
parents:
diff changeset
428 "display order":1
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iuc
parents:
diff changeset
429 },
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
430 "Rate classes":{
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iuc
parents:
diff changeset
431 "attribute type":"branch label",
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iuc
parents:
diff changeset
432 "display order":2
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
433 },
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iuc
parents:
diff changeset
434 "Full adaptive model":{
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iuc
parents:
diff changeset
435 "attribute type":"branch length",
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iuc
parents:
diff changeset
436 "display order":2
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
437 },
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
438 "Rate Distributions":{
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iuc
parents:
diff changeset
439 "attribute type":"branch label",
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
440 "display order":3
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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441 },
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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442 "LRT":{
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
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443 "attribute type":"branch label",
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
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444 "display order":4
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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445 },
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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446 "Uncorrected P-value":{
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
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447 "attribute type":"branch label",
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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448 "display order":5
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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449 },
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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450 "Corrected P-value":{
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
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451 "attribute type":"branch label",
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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452 "display order":6
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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453 }
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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454 }
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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455 }
fe399429a5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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456 }