Mercurial > repos > iuc > hyphy_slac

annotate test-data/absrel-out1.json @ 31:c010cbc8ff3a 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 9ef881c2d3d5f240cbff33667b55f72cb82d9896"
author iuc
date Tue, 05 Oct 2021 05:01:47 +0000
parents d6f4ff2aed07
children
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9da003917dcb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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1 {
9da003917dcb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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2 "analysis":{
9da003917dcb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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3 "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
16
d6f4ff2aed07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"
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4 "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. v2.2 adds support for multiple-hit models",
0
9da003917dcb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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5 "contact":"spond@temple.edu",
16
d6f4ff2aed07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"
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6 "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.",
d6f4ff2aed07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"
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7 "requirements":"in-frame codon alignment and a phylogenetic tree",
d6f4ff2aed07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"
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8 "version":"2.2"
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9da003917dcb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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9 },
9da003917dcb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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10 "branch attributes":{
9da003917dcb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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11 "0":{
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12 "Baboon":{
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13 "Baseline MG94xREV":0.001816807585564731,
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14 "Baseline MG94xREV omega ratio":0,
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15 "Corrected P-value":1,
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16 "Full adaptive model":0.001810407118394509,
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9da003917dcb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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17 "LRT":0,
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18 "Nucleotide GTR":0.001678881906620672,
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19 "Rate Distributions": [
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20 [0, 1]
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9da003917dcb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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21 ],
9da003917dcb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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22 "Rate classes":1,
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23 "Uncorrected P-value":1,
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24 "original name":"Baboon",
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25 "rate at which 2 nucleotides are changed instantly within a single codon":0
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26 },
9da003917dcb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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27 "Cat":{
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28 "Baseline MG94xREV":0.2286001363527903,
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29 "Baseline MG94xREV omega ratio":1.403298474422089,
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30 "Corrected P-value":1,
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31 "Full adaptive model":0.1219386838393392,
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32 "LRT":1.644967676056694,
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33 "Nucleotide GTR":0.265904547400163,
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34 "Rate Distributions": [
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35 [0.2130519766306851, 0.6352283641519592],
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36 [2.628217450705319, 0.3647716358480408]
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37 ],
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9da003917dcb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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38 "Rate classes":2,
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39 "Uncorrected P-value":0.171730764045231,
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40 "original name":"Cat",
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41 "rate at which 2 nucleotides are changed instantly within a single codon":0
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42 },
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43 "Chimp":{
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44 "Baseline MG94xREV":0.001840311209746262,
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45 "Baseline MG94xREV omega ratio":10000000000,
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46 "Corrected P-value":1,
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47 "Full adaptive model":0.001841979303044237,
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48 "LRT":0.6159123786974305,
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49 "Nucleotide GTR":0.001816713800925801,
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50 "Rate Distributions": [
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51 [10000000000, 1]
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52 ],
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53 "Rate classes":1,
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54 "Uncorrected P-value":0.3069983227523322,
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55 "original name":"Chimp",
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56 "rate at which 2 nucleotides are changed instantly within a single codon":0
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57 },
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58 "Cow":{
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59 "Baseline MG94xREV":0.2070244948790512,
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60 "Baseline MG94xREV omega ratio":2.153434974462683,
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61 "Corrected P-value":0.5006146299996015,
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62 "Full adaptive model":0.1241125417707662,
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63 "LRT":4.898194538953248,
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64 "Nucleotide GTR":0.2481512612523618,
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65 "Rate Distributions": [
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67 [2.444056517734385, 0.47681273559051]
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68 ],
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69 "Rate classes":2,
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70 "Uncorrected P-value":0.03128841437497509,
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71 "original name":"Cow",
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72 "rate at which 2 nucleotides are changed instantly within a single codon":0
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73 },
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74 "Horse":{
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75 "Baseline MG94xREV":0.190365915457708,
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76 "Baseline MG94xREV omega ratio":1.182933895494305,
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77 "Corrected P-value":1,
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78 "Full adaptive model":0.0869489794025302,
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79 "LRT":2.047309801283518,
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80 "Nucleotide GTR":0.2090927256979082,
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81 "Rate Distributions": [
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83 [1.633257246666139, 0.4602341921752869]
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85 "Rate classes":2,
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86 "Uncorrected P-value":0.1382789032066179,
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87 "original name":"Horse",
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88 "rate at which 2 nucleotides are changed instantly within a single codon":0
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89 },
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90 "Human":{
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91 "Baseline MG94xREV":0,
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92 "Baseline MG94xREV omega ratio":1,
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93 "Corrected P-value":1,
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94 "Full adaptive model":0,
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95 "LRT":0,
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96 "Nucleotide GTR":0,
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97 "Rate Distributions": [
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98 [1, 1]
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100 "Rate classes":1,
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101 "Uncorrected P-value":1,
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102 "original name":"Human",
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103 "rate at which 2 nucleotides are changed instantly within a single codon":0.0006106118725184574
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105 "Mouse":{
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106 "Baseline MG94xREV":0.1083167307250788,
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107 "Baseline MG94xREV omega ratio":0.5108576904540283,
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108 "Corrected P-value":1,
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109 "Full adaptive model":0.1078010043714489,
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110 "LRT":0,
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111 "Nucleotide GTR":0.1181001275359051,
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112 "Rate Distributions": [
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115 "Rate classes":1,
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117 "original name":"Mouse",
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118 "rate at which 2 nucleotides are changed instantly within a single codon":0.4244832903005548
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119 },
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120 "Node1":{
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121 "Baseline MG94xREV":0.2542393300501047,
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122 "Baseline MG94xREV omega ratio":0.2997498382776075,
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123 "Corrected P-value":1,
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124 "Full adaptive model":0.2550466752020236,
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125 "LRT":0,
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126 "Nucleotide GTR":0.2767426965701868,
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127 "Rate Distributions": [
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128 [0.2932817609633239, 1]
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130 "Rate classes":1,
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131 "Uncorrected P-value":1,
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132 "rate at which 2 nucleotides are changed instantly within a single codon":0.9114373463003921
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133 },
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134 "Node12":{
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135 "Baseline MG94xREV":0.01400815185374474,
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136 "Baseline MG94xREV omega ratio":0.2754467062829232,
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137 "Corrected P-value":1,
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138 "Full adaptive model":0.01437973904273591,
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139 "LRT":0,
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140 "Nucleotide GTR":0.01784721909304638,
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141 "Rate Distributions": [
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142 [0.3037614070859027, 1]
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144 "Rate classes":1,
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145 "Uncorrected P-value":1,
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146 "rate at which 2 nucleotides are changed instantly within a single codon":0.5084909616267814
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147 },
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148 "Node2":{
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149 "Baseline MG94xREV":0.0400106272595141,
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150 "Baseline MG94xREV omega ratio":0.116408812566168,
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151 "Corrected P-value":1,
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152 "Full adaptive model":0.03991940069030483,
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153 "LRT":0,
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154 "Nucleotide GTR":0.06613304839358287,
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155 "Rate Distributions": [
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156 [0.1193993042178124, 1]
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158 "Rate classes":1,
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159 "Uncorrected P-value":1,
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160 "rate at which 2 nucleotides are changed instantly within a single codon":9.28646275825122
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161 },
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162 "Node3":{
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163 "Baseline MG94xREV":0.08548068002443369,
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164 "Baseline MG94xREV omega ratio":1.293385437932658,
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165 "Corrected P-value":1,
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166 "Full adaptive model":0.08590119038008139,
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167 "LRT":0.1383887036890883,
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168 "Nucleotide GTR":0.09881178513658169,
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169 "Rate Distributions": [
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170 [1.330576641567385, 1]
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172 "Rate classes":1,
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173 "Uncorrected P-value":0.4219212196398351,
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174 "rate at which 2 nucleotides are changed instantly within a single codon":0.8390789546113498
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iuc
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diff changeset
175 },
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diff changeset
176 "Node8":{
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177 "Baseline MG94xREV":0.09463393920061362,
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178 "Baseline MG94xREV omega ratio":1.862136443854597,
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179 "Corrected P-value":1,
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180 "Full adaptive model":0.0958035263641453,
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181 "LRT":0.7150293976401372,
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182 "Nucleotide GTR":0.1062333225692588,
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183 "Rate Distributions": [
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184 [1.883870769808856, 1]
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185 ],
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186 "Rate classes":1,
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187 "Uncorrected P-value":0.2893795680778183,
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188 "rate at which 2 nucleotides are changed instantly within a single codon":0.512238843416092
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189 },
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190 "Node9":{
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191 "Baseline MG94xREV":0.02846111726225027,
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192 "Baseline MG94xREV omega ratio":0.4321055128385307,
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193 "Corrected P-value":1,
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194 "Full adaptive model":0.02810856974543091,
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195 "LRT":0,
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196 "Nucleotide GTR":0.02566185438854229,
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197 "Rate Distributions": [
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198 [0.4185836885800617, 1]
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199 ],
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200 "Rate classes":1,
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201 "Uncorrected P-value":1,
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202 "rate at which 2 nucleotides are changed instantly within a single codon":0
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203 },
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204 "Pig":{
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205 "Baseline MG94xREV":0.1782835053555321,
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206 "Baseline MG94xREV omega ratio":1.275728452678247,
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207 "Corrected P-value":1,
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208 "Full adaptive model":0.1729188354138871,
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iuc
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diff changeset
209 "LRT":0.3324036585026988,
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iuc
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210 "Nucleotide GTR":0.1871760137183495,
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211 "Rate Distributions": [
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212 [1.235108129487059, 1]
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213 ],
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214 "Rate classes":1,
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215 "Uncorrected P-value":0.3669120164240152,
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216 "original name":"Pig",
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diff changeset
217 "rate at which 2 nucleotides are changed instantly within a single codon":0.1143447431158695
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218 },
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diff changeset
219 "Rat":{
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220 "Baseline MG94xREV":0.06315403896300904,
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221 "Baseline MG94xREV omega ratio":0.8744850915248316,
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222 "Corrected P-value":1,
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iuc
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223 "Full adaptive model":0.06408078523886611,
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diff changeset
224 "LRT":0,
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225 "Nucleotide GTR":0.0666364425850592,
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226 "Rate Distributions": [
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227 [0.8782045320352186, 1]
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228 ],
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229 "Rate classes":1,
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230 "Uncorrected P-value":1,
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231 "original name":"Rat",
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232 "rate at which 2 nucleotides are changed instantly within a single codon":0.1346164190615118
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233 },
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diff changeset
234 "RhMonkey":{
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235 "Baseline MG94xREV":0.003671939837747083,
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diff changeset
236 "Baseline MG94xREV omega ratio":10000000000,
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iuc
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diff changeset
237 "Corrected P-value":1,
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iuc
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diff changeset
238 "Full adaptive model":0.003675047654636179,
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iuc
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diff changeset
239 "LRT":1.165062770327495,
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iuc
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diff changeset
240 "Nucleotide GTR":0.003777016173741061,
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241 "Rate Distributions": [
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diff changeset
242 [10000000000, 1]
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243 ],
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244 "Rate classes":1,
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245 "Uncorrected P-value":0.2236284592802686,
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diff changeset
246 "original name":"RhMonkey",
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247 "rate at which 2 nucleotides are changed instantly within a single codon":0
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iuc
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248 }
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iuc
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249 },
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iuc
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250 "attributes":{
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251 "Baseline MG94xREV":{
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iuc
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252 "attribute type":"branch length",
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iuc
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253 "display order":1
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iuc
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254 },
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iuc
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255 "Baseline MG94xREV omega ratio":{
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iuc
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256 "attribute type":"branch label",
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iuc
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257 "display order":1
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258 },
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259 "Corrected P-value":{
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iuc
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260 "attribute type":"branch label",
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261 "display order":6
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262 },
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iuc
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263 "Full adaptive model":{
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264 "attribute type":"branch length",
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265 "display order":2
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266 },
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267 "LRT":{
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268 "attribute type":"branch label",
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269 "display order":4
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270 },
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271 "Nucleotide GTR":{
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272 "attribute type":"branch length",
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273 "display order":0
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274 },
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275 "Rate Distributions":{
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276 "attribute type":"branch label",
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277 "display order":3
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278 },
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279 "Rate classes":{
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280 "attribute type":"branch label",
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281 "display order":2
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283 "Uncorrected P-value":{
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287 "original name":{
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290 },
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291 "rate at which 2 nucleotides are changed instantly within a single codon":{
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294 }
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295 }
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297 "data partitions":{
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298 "0":{
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299 "coverage": [
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300 [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]
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302 "name":"absrel.filter.default"
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303 }
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304 },
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305 "fits":{
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306 "Baseline MG94xREV":{
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307 "AIC-c":6983.763305606333,
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308 "Equilibrium frequencies": [
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364 [0.009471947420992787],
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369 [0.01188403168729233]
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370 ],
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diff changeset
371 "Log Likelihood":-3427.720059001285,
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372 "Rate Distributions":{
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373 "Per-branch delta":{
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374 "2.5%":0,
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375 "97.5%":12.07373117808175,
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376 "Mean":1.277646334033236,
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377 "Median":0.4551223038316586
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378 },
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379 "Per-branch omega":{
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380 "2.5%":0,
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381 "97.5%":2.153434974462683,
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382 "Mean":666666667.5119981,
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383 "Median":1
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384 }
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385 },
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386 "display order":1,
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387 "estimated parameters":62
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388 },
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diff changeset
389 "Full adaptive model":{
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iuc
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390 "AIC-c":6972.859938351839,
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iuc
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391 "Log Likelihood":-3415.824749853321,
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iuc
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392 "Rate Distributions":{
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393 },
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394 "display order":2,
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395 "estimated parameters":68
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396 },
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397 "Nucleotide GTR":{
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398 "AIC-c":7112.857317645923,
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399 "Equilibrium frequencies": [
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400 [0.3592490842490842],
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401 [0.181959706959707],
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402 [0.240018315018315],
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403 [0.2187728937728937]
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404 ],
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405 "Log Likelihood":-3532.321228205235,
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406 "Rate Distributions":{
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407 "Substitution rate from nucleotide A to nucleotide C":0.5498703043473002,
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408 "Substitution rate from nucleotide A to nucleotide G":1,
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409 "Substitution rate from nucleotide A to nucleotide T":0.2646979624678532,
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diff changeset
410 "Substitution rate from nucleotide C to nucleotide G":0.4921328068285813,
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411 "Substitution rate from nucleotide C to nucleotide T":1.028960084526602,
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412 "Substitution rate from nucleotide G to nucleotide T":0.3044365000595399
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413 },
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414 "display order":0,
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diff changeset
415 "estimated parameters":24
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416 }
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417 },
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diff changeset
418 "input":{
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diff changeset
419 "file name":"/tmp/tmpx_42i6f0/job_working_directory/000/6/working/./absrel_input.fa",
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diff changeset
420 "number of sequences":10,
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diff changeset
421 "number of sites":187,
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diff changeset
422 "partition count":1,
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diff changeset
423 "trees":{
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iuc
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diff changeset
424 "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,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)"
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425 }
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426 },
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diff changeset
427 "test results":{
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diff changeset
428 "P-value threshold":0.05,
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diff changeset
429 "positive test results":0,
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diff changeset
430 "tested":16
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431 },
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diff changeset
432 "tested":{
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diff changeset
433 "0":{
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iuc
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diff changeset
434 "Baboon":"test",
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iuc
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diff changeset
435 "Cat":"test",
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iuc
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diff changeset
436 "Chimp":"test",
d6f4ff2aed07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"
iuc
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diff changeset
437 "Cow":"test",
d6f4ff2aed07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"
iuc
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diff changeset
438 "Horse":"test",
d6f4ff2aed07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"
iuc
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diff changeset
439 "Human":"test",
d6f4ff2aed07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"
iuc
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diff changeset
440 "Mouse":"test",
d6f4ff2aed07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"
iuc
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diff changeset
441 "Node1":"test",
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iuc
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diff changeset
442 "Node12":"test",
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443 "Node2":"test",
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444 "Node3":"test",
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445 "Node8":"test",
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446 "Node9":"test",
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447 "Pig":"test",
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448 "Rat":"test",
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449 "RhMonkey":"test"
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450 }
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451 },
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452 "timers":{
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453 "Baseline model fitting":{
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454 "order":2,
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455 "timer":17
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456 },
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457 "Complexity analysis":{
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458 "order":3,
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459 "timer":110
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460 },
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461 "Full adaptive model fitting":{
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462 "order":4,
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463 "timer":20
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464 },
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465 "Overall":{
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466 "order":0,
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467 "timer":259
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468 },
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469 "Preliminary model fitting":{
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470 "order":1,
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471 "timer":0
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472 },
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473 "Testing for selection":{
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474 "order":5,
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475 "timer":112
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476 }
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477 }
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478 }