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1 <?xml version="1.0" ?>
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2 <tool id="qiime_phylogeny_iqtree-ultrafast-bootstrap" name="qiime phylogeny iqtree-ultrafast-bootstrap"
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3 version="2020.8">
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4 <description>Construct a phylogenetic tree with IQ-TREE with bootstrap supports.</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime phylogeny iqtree-ultrafast-bootstrap
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10
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11 --i-alignment=$ialignment
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12
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13 #if str($pseed):
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14 --p-seed=$pseed
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15 #end if
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16 #if str($pncores) != 'None':
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17 --p-n-cores=$pncores
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18 #end if
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19
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20 #set $pncoresmax = '${GALAXY_SLOTS:-4}'
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21
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22 #if str($pncoresmax):
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23 --p-n-cores-max=$pncoresmax
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24 #end if
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25
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26 --p-n-runs=$pnruns
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27
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28 #if str($psubstitutionmodel) != 'None':
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29 --p-substitution-model=$psubstitutionmodel
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30 #end if
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31
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32 --p-bootstrap-replicates=$pbootstrapreplicates
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33
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34 #if str($pninitparstrees):
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35 --p-n-init-pars-trees=$pninitparstrees
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36 #end if
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37 #if str($pntopinittrees):
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38 --p-n-top-init-trees=$pntopinittrees
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39 #end if
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40 #if str($pnbestretaintrees):
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41 --p-n-best-retain-trees=$pnbestretaintrees
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42 #end if
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43 #if str($pstopiter):
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44 --p-stop-iter=$pstopiter
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45 #end if
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46 #if str($pperturbnnistrength):
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47 --p-perturb-nni-strength=$pperturbnnistrength
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48 #end if
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49 #if str($psprradius):
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50 --p-spr-radius=$psprradius
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51 #end if
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52 #if str($pnmaxufbootiter):
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53 --p-n-max-ufboot-iter=$pnmaxufbootiter
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54 #end if
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55 #if str($pnufbootsteps):
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56 --p-n-ufboot-steps=$pnufbootsteps
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57 #end if
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58 #if str($pmincorufboot):
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59 --p-min-cor-ufboot=$pmincorufboot
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60 #end if
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61 #if str($pepbreakufboot):
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62 --p-ep-break-ufboot=$pepbreakufboot
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63 #end if
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64 #if $pallnni:
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65 --p-allnni
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66 #end if
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67
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68 #if str($palrt):
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69 --p-alrt=$palrt
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70 #end if
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71 #if $pabayes:
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72 --p-abayes
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73 #end if
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74
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75 #if str($plbp):
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76 --p-lbp=$plbp
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77 #end if
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78 #if $pbnni:
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79 --p-bnni
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80 #end if
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81
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82 #if $psafe:
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83 --p-safe
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84 #end if
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85
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86 --o-tree=otree
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87
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88 #if str($examples) != 'None':
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89 --examples=$examples
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90 #end if
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91
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92 ;
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93 cp otree.qza $otree
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94
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95 ]]></command>
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96 <inputs>
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97 <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction. [required]" name="ialignment" optional="False" type="data" />
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98 <param label="--p-seed: INTEGER Random number seed. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pseed" optional="False" type="text" />
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99 <param label="--p-n-cores: " name="pncores" optional="True" type="select">
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100 <option selected="True" value="None">Selection is Optional</option>
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101 <option value="Int % Range(1">Int % Range(1</option>
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102 <option value="None">None</option>
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103 </param>
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104 <param label="--p-n-runs: INTEGER Number of indepedent runs. Multiple independent Range(1, None) runs (e.g. 10) can outperform a single run in terms of likelihood maximisation. [default: 1]" min="1" name="pnruns" optional="True" type="integer" value="1" />
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105 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
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106 <option selected="True" value="None">Selection is Optional</option>
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107 <option value="JC">JC</option>
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108 <option value="JC+I">JC+I</option>
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109 <option value="JC+G">JC+G</option>
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110 <option value="JC+I+G">JC+I+G</option>
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111 <option value="JC+R2">JC+R2</option>
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112 <option value="JC+R3">JC+R3</option>
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113 <option value="JC+R4">JC+R4</option>
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114 <option value="JC+R5">JC+R5</option>
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115 <option value="JC+R6">JC+R6</option>
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116 <option value="JC+R7">JC+R7</option>
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117 <option value="JC+R8">JC+R8</option>
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118 <option value="JC+R9">JC+R9</option>
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119 <option value="JC+R10">JC+R10</option>
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120 <option value="F81">F81</option>
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121 <option value="F81+I">F81+I</option>
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122 <option value="F81+G">F81+G</option>
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123 <option value="F81+I+G">F81+I+G</option>
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124 <option value="F81+R2">F81+R2</option>
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125 <option value="F81+R3">F81+R3</option>
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126 <option value="F81+R4">F81+R4</option>
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127 <option value="F81+R5">F81+R5</option>
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128 <option value="F81+R6">F81+R6</option>
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129 <option value="F81+R7">F81+R7</option>
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130 <option value="F81+R8">F81+R8</option>
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131 <option value="F81+R9">F81+R9</option>
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132 <option value="F81+R10">F81+R10</option>
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133 <option value="K80">K80</option>
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134 <option value="K80+I">K80+I</option>
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135 <option value="K80+G">K80+G</option>
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136 <option value="K80+I+G">K80+I+G</option>
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137 <option value="K80+R2">K80+R2</option>
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138 <option value="K80+R3">K80+R3</option>
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139 <option value="K80+R4">K80+R4</option>
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140 <option value="K80+R5">K80+R5</option>
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141 <option value="K80+R6">K80+R6</option>
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142 <option value="K80+R7">K80+R7</option>
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143 <option value="K80+R8">K80+R8</option>
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144 <option value="K80+R9">K80+R9</option>
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145 <option value="K80+R10">K80+R10</option>
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146 <option value="HKY">HKY</option>
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147 <option value="HKY+I">HKY+I</option>
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148 <option value="HKY+G">HKY+G</option>
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149 <option value="HKY+I+G">HKY+I+G</option>
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150 <option value="HKY+R2">HKY+R2</option>
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151 <option value="HKY+R3">HKY+R3</option>
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152 <option value="HKY+R4">HKY+R4</option>
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153 <option value="HKY+R5">HKY+R5</option>
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154 <option value="HKY+R6">HKY+R6</option>
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155 <option value="HKY+R7">HKY+R7</option>
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156 <option value="HKY+R8">HKY+R8</option>
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157 <option value="HKY+R9">HKY+R9</option>
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158 <option value="HKY+R10">HKY+R10</option>
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159 <option value="TNe">TNe</option>
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160 <option value="TNe+I">TNe+I</option>
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161 <option value="TNe+G">TNe+G</option>
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162 <option value="TNe+I+G">TNe+I+G</option>
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163 <option value="TNe+R2">TNe+R2</option>
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164 <option value="TNe+R3">TNe+R3</option>
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165 <option value="TNe+R4">TNe+R4</option>
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166 <option value="TNe+R5">TNe+R5</option>
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167 <option value="TNe+R6">TNe+R6</option>
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168 <option value="TNe+R7">TNe+R7</option>
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169 <option value="TNe+R8">TNe+R8</option>
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170 <option value="TNe+R9">TNe+R9</option>
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171 <option value="TNe+R10">TNe+R10</option>
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172 <option value="TN">TN</option>
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173 <option value="TN+I">TN+I</option>
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174 <option value="TN+G">TN+G</option>
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175 <option value="TN+I+G">TN+I+G</option>
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176 <option value="TN+R2">TN+R2</option>
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177 <option value="TN+R3">TN+R3</option>
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178 <option value="TN+R4">TN+R4</option>
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179 <option value="TN+R5">TN+R5</option>
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180 <option value="TN+R6">TN+R6</option>
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181 <option value="TN+R7">TN+R7</option>
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182 <option value="TN+R8">TN+R8</option>
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183 <option value="TN+R9">TN+R9</option>
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184 <option value="TN+R10">TN+R10</option>
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185 <option value="K81">K81</option>
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186 <option value="K81+I">K81+I</option>
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187 <option value="K81+G">K81+G</option>
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188 <option value="K81+I+G">K81+I+G</option>
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189 <option value="K81+R2">K81+R2</option>
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190 <option value="K81+R3">K81+R3</option>
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191 <option value="K81+R4">K81+R4</option>
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192 <option value="K81+R5">K81+R5</option>
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193 <option value="K81+R6">K81+R6</option>
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194 <option value="K81+R7">K81+R7</option>
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195 <option value="K81+R8">K81+R8</option>
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196 <option value="K81+R9">K81+R9</option>
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197 <option value="K81+R10">K81+R10</option>
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198 <option value="K81u">K81u</option>
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199 <option value="K81u+I">K81u+I</option>
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200 <option value="K81u+G">K81u+G</option>
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201 <option value="K81u+I+G">K81u+I+G</option>
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202 <option value="K81u+R2">K81u+R2</option>
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203 <option value="K81u+R3">K81u+R3</option>
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204 <option value="K81u+R4">K81u+R4</option>
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205 <option value="K81u+R5">K81u+R5</option>
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206 <option value="K81u+R6">K81u+R6</option>
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207 <option value="K81u+R7">K81u+R7</option>
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208 <option value="K81u+R8">K81u+R8</option>
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209 <option value="K81u+R9">K81u+R9</option>
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210 <option value="K81u+R10">K81u+R10</option>
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211 <option value="TPM2">TPM2</option>
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212 <option value="TPM2+I">TPM2+I</option>
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213 <option value="TPM2+G">TPM2+G</option>
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214 <option value="TPM2+I+G">TPM2+I+G</option>
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215 <option value="TPM2+R2">TPM2+R2</option>
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216 <option value="TPM2+R3">TPM2+R3</option>
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217 <option value="TPM2+R4">TPM2+R4</option>
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218 <option value="TPM2+R5">TPM2+R5</option>
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219 <option value="TPM2+R6">TPM2+R6</option>
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220 <option value="TPM2+R7">TPM2+R7</option>
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221 <option value="TPM2+R8">TPM2+R8</option>
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222 <option value="TPM2+R9">TPM2+R9</option>
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223 <option value="TPM2+R10">TPM2+R10</option>
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224 <option value="TPM2u">TPM2u</option>
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225 <option value="TPM2u+I">TPM2u+I</option>
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226 <option value="TPM2u+G">TPM2u+G</option>
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227 <option value="TPM2u+I+G">TPM2u+I+G</option>
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228 <option value="TPM2u+R2">TPM2u+R2</option>
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229 <option value="TPM2u+R3">TPM2u+R3</option>
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230 <option value="TPM2u+R4">TPM2u+R4</option>
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231 <option value="TPM2u+R5">TPM2u+R5</option>
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232 <option value="TPM2u+R6">TPM2u+R6</option>
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233 <option value="TPM2u+R7">TPM2u+R7</option>
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234 <option value="TPM2u+R8">TPM2u+R8</option>
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235 <option value="TPM2u+R9">TPM2u+R9</option>
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236 <option value="TPM2u+R10">TPM2u+R10</option>
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237 <option value="TPM3">TPM3</option>
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238 <option value="TPM3+I">TPM3+I</option>
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239 <option value="TPM3+G">TPM3+G</option>
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240 <option value="TPM3+I+G">TPM3+I+G</option>
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241 <option value="TPM3+R2">TPM3+R2</option>
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242 <option value="TPM3+R3">TPM3+R3</option>
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243 <option value="TPM3+R4">TPM3+R4</option>
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244 <option value="TPM3+R5">TPM3+R5</option>
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245 <option value="TPM3+R6">TPM3+R6</option>
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246 <option value="TPM3+R7">TPM3+R7</option>
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247 <option value="TPM3+R8">TPM3+R8</option>
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248 <option value="TPM3+R9">TPM3+R9</option>
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249 <option value="TPM3+R10">TPM3+R10</option>
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250 <option value="TPM3u">TPM3u</option>
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251 <option value="TPM3u+I">TPM3u+I</option>
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252 <option value="TPM3u+G">TPM3u+G</option>
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253 <option value="TPM3u+I+G">TPM3u+I+G</option>
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254 <option value="TPM3u+R2">TPM3u+R2</option>
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255 <option value="TPM3u+R3">TPM3u+R3</option>
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256 <option value="TPM3u+R4">TPM3u+R4</option>
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257 <option value="TPM3u+R5">TPM3u+R5</option>
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258 <option value="TPM3u+R6">TPM3u+R6</option>
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259 <option value="TPM3u+R7">TPM3u+R7</option>
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260 <option value="TPM3u+R8">TPM3u+R8</option>
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261 <option value="TPM3u+R9">TPM3u+R9</option>
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262 <option value="TPM3u+R10">TPM3u+R10</option>
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263 <option value="TIMe">TIMe</option>
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264 <option value="TIMe+I">TIMe+I</option>
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265 <option value="TIMe+G">TIMe+G</option>
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266 <option value="TIMe+I+G">TIMe+I+G</option>
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267 <option value="TIMe+R2">TIMe+R2</option>
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268 <option value="TIMe+R3">TIMe+R3</option>
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269 <option value="TIMe+R4">TIMe+R4</option>
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270 <option value="TIMe+R5">TIMe+R5</option>
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271 <option value="TIMe+R6">TIMe+R6</option>
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272 <option value="TIMe+R7">TIMe+R7</option>
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273 <option value="TIMe+R8">TIMe+R8</option>
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274 <option value="TIMe+R9">TIMe+R9</option>
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275 <option value="TIMe+R10">TIMe+R10</option>
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276 <option value="TIM">TIM</option>
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277 <option value="TIM+I">TIM+I</option>
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278 <option value="TIM+G">TIM+G</option>
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279 <option value="TIM+I+G">TIM+I+G</option>
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280 <option value="TIM+R2">TIM+R2</option>
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281 <option value="TIM+R3">TIM+R3</option>
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282 <option value="TIM+R4">TIM+R4</option>
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283 <option value="TIM+R5">TIM+R5</option>
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284 <option value="TIM+R6">TIM+R6</option>
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285 <option value="TIM+R7">TIM+R7</option>
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286 <option value="TIM+R8">TIM+R8</option>
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287 <option value="TIM+R9">TIM+R9</option>
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288 <option value="TIM+R10">TIM+R10</option>
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289 <option value="TIM2e">TIM2e</option>
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290 <option value="TIM2e+I">TIM2e+I</option>
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291 <option value="TIM2e+G">TIM2e+G</option>
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292 <option value="TIM2e+I+G">TIM2e+I+G</option>
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293 <option value="TIM2e+R2">TIM2e+R2</option>
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294 <option value="TIM2e+R3">TIM2e+R3</option>
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295 <option value="TIM2e+R4">TIM2e+R4</option>
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296 <option value="TIM2e+R5">TIM2e+R5</option>
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297 <option value="TIM2e+R6">TIM2e+R6</option>
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298 <option value="TIM2e+R7">TIM2e+R7</option>
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299 <option value="TIM2e+R8">TIM2e+R8</option>
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300 <option value="TIM2e+R9">TIM2e+R9</option>
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301 <option value="TIM2e+R10">TIM2e+R10</option>
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302 <option value="TIM2">TIM2</option>
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303 <option value="TIM2+I">TIM2+I</option>
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304 <option value="TIM2+G">TIM2+G</option>
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305 <option value="TIM2+I+G">TIM2+I+G</option>
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306 <option value="TIM2+R2">TIM2+R2</option>
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307 <option value="TIM2+R3">TIM2+R3</option>
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308 <option value="TIM2+R4">TIM2+R4</option>
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309 <option value="TIM2+R5">TIM2+R5</option>
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310 <option value="TIM2+R6">TIM2+R6</option>
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311 <option value="TIM2+R7">TIM2+R7</option>
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312 <option value="TIM2+R8">TIM2+R8</option>
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313 <option value="TIM2+R9">TIM2+R9</option>
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314 <option value="TIM2+R10">TIM2+R10</option>
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315 <option value="TIM3e">TIM3e</option>
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316 <option value="TIM3e+I">TIM3e+I</option>
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317 <option value="TIM3e+G">TIM3e+G</option>
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318 <option value="TIM3e+I+G">TIM3e+I+G</option>
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319 <option value="TIM3e+R2">TIM3e+R2</option>
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320 <option value="TIM3e+R3">TIM3e+R3</option>
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321 <option value="TIM3e+R4">TIM3e+R4</option>
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322 <option value="TIM3e+R5">TIM3e+R5</option>
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323 <option value="TIM3e+R6">TIM3e+R6</option>
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324 <option value="TIM3e+R7">TIM3e+R7</option>
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325 <option value="TIM3e+R8">TIM3e+R8</option>
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326 <option value="TIM3e+R9">TIM3e+R9</option>
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327 <option value="TIM3e+R10">TIM3e+R10</option>
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328 <option value="TIM3">TIM3</option>
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329 <option value="TIM3+I">TIM3+I</option>
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330 <option value="TIM3+G">TIM3+G</option>
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331 <option value="TIM3+I+G">TIM3+I+G</option>
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332 <option value="TIM3+R2">TIM3+R2</option>
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333 <option value="TIM3+R3">TIM3+R3</option>
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334 <option value="TIM3+R4">TIM3+R4</option>
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335 <option value="TIM3+R5">TIM3+R5</option>
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336 <option value="TIM3+R6">TIM3+R6</option>
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337 <option value="TIM3+R7">TIM3+R7</option>
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338 <option value="TIM3+R8">TIM3+R8</option>
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339 <option value="TIM3+R9">TIM3+R9</option>
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340 <option value="TIM3+R10">TIM3+R10</option>
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341 <option value="TVMe">TVMe</option>
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342 <option value="TVMe+I">TVMe+I</option>
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343 <option value="TVMe+G">TVMe+G</option>
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344 <option value="TVMe+I+G">TVMe+I+G</option>
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345 <option value="TVMe+R2">TVMe+R2</option>
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346 <option value="TVMe+R3">TVMe+R3</option>
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347 <option value="TVMe+R4">TVMe+R4</option>
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348 <option value="TVMe+R5">TVMe+R5</option>
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349 <option value="TVMe+R6">TVMe+R6</option>
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350 <option value="TVMe+R7">TVMe+R7</option>
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351 <option value="TVMe+R8">TVMe+R8</option>
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352 <option value="TVMe+R9">TVMe+R9</option>
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353 <option value="TVMe+R10">TVMe+R10</option>
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354 <option value="TVM">TVM</option>
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355 <option value="TVM+I">TVM+I</option>
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356 <option value="TVM+G">TVM+G</option>
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357 <option value="TVM+I+G">TVM+I+G</option>
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358 <option value="TVM+R2">TVM+R2</option>
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359 <option value="TVM+R3">TVM+R3</option>
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360 <option value="TVM+R4">TVM+R4</option>
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361 <option value="TVM+R5">TVM+R5</option>
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362 <option value="TVM+R6">TVM+R6</option>
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363 <option value="TVM+R7">TVM+R7</option>
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364 <option value="TVM+R8">TVM+R8</option>
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365 <option value="TVM+R9">TVM+R9</option>
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366 <option value="TVM+R10">TVM+R10</option>
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367 <option value="SYM">SYM</option>
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368 <option value="SYM+I">SYM+I</option>
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369 <option value="SYM+G">SYM+G</option>
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370 <option value="SYM+I+G">SYM+I+G</option>
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371 <option value="SYM+R2">SYM+R2</option>
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372 <option value="SYM+R3">SYM+R3</option>
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373 <option value="SYM+R4">SYM+R4</option>
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374 <option value="SYM+R5">SYM+R5</option>
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375 <option value="SYM+R6">SYM+R6</option>
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376 <option value="SYM+R7">SYM+R7</option>
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377 <option value="SYM+R8">SYM+R8</option>
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378 <option value="SYM+R9">SYM+R9</option>
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379 <option value="SYM+R10">SYM+R10</option>
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380 <option value="GTR">GTR</option>
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381 <option value="GTR+I">GTR+I</option>
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382 <option value="GTR+G">GTR+G</option>
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383 <option value="GTR+I+G">GTR+I+G</option>
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384 <option value="GTR+R2">GTR+R2</option>
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385 <option value="GTR+R3">GTR+R3</option>
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386 <option value="GTR+R4">GTR+R4</option>
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387 <option value="GTR+R5">GTR+R5</option>
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388 <option value="GTR+R6">GTR+R6</option>
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389 <option value="GTR+R7">GTR+R7</option>
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390 <option value="GTR+R8">GTR+R8</option>
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391 <option value="GTR+R9">GTR+R9</option>
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392 <option value="GTR+R10">GTR+R10</option>
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393 <option value="MFP">MFP</option>
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394 <option value="TEST">TEST</option>
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395 </param>
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396 <param label="--p-bootstrap-replicates: INTEGER Range(1000, None) The number of bootstrap searches to perform. Minimum of 1000 recomended. [default: 1000]" min="1000" name="pbootstrapreplicates" optional="True" type="integer" value="1000" />
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397 <param label="--p-n-init-pars-trees: INTEGER Range(1, None) Number of initial parsimony trees. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pninitparstrees" optional="False" type="text" />
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398 <param label="--p-n-top-init-trees: INTEGER Range(1, None) Number of top initial trees. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pntopinittrees" optional="False" type="text" />
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399 <param label="--p-n-best-retain-trees: INTEGER Range(1, None) Number of best trees retained during search. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pnbestretaintrees" optional="False" type="text" />
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400 <param label="--p-stop-iter: INTEGER Number of unsuccessful iterations to stop. If not Range(1, None) set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pstopiter" optional="False" type="text" />
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|
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401 <param label="--p-perturb-nni-strength: NUMBER Range(0.01, 1.0) Perturbation strength for randomized NNI. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pperturbnnistrength" optional="False" type="text" />
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402 <param label="--p-spr-radius: INTEGER Radius for parsimony SPR search. If not set, Range(1, None) program defaults will be used. See IQ-TREE manual for details. [optional]" name="psprradius" optional="False" type="text" />
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|
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403 <param label="--p-n-max-ufboot-iter: INTEGER Range(1, None) Maximum number of iterations. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pnmaxufbootiter" optional="False" type="text" />
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404 <param label="--p-n-ufboot-steps: INTEGER Range(1, None) Number of iterations for UFBoot stopping rule. If not set, program defaults will be used.See IQ-TREE manual for details. [optional]" name="pnufbootsteps" optional="False" type="text" />
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405 <param label="--p-min-cor-ufboot: NUMBER Range(0.51, 0.99) Minimum correlation coefficient. If not set, program defaults will be used.See IQ-TREE manual for details. [optional]" name="pmincorufboot" optional="False" type="text" />
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|
406 <param label="--p-ep-break-ufboot: NUMBER Range(0.01, 0.99) Epsilon value to break tie. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pepbreakufboot" optional="False" type="text" />
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|
407 <param label="--p-allnni: --p-allnni: / --p-no-allnni Perform more thorough NNI search. [default: False]" name="pallnni" selected="False" type="boolean" />
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|
|
408 <param label="--p-alrt: INTEGER Single branch test method. Number of bootstrap Range(1000, None) replicates to perform an SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 replicates is recomended. Can be used with other \'single branch test methods\'. Values reported in the order of: alrt, lbp, abayes. [optional]" name="palrt" optional="False" type="text" />
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|
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409 <param label="--p-abayes: --p-abayes: / --p-no-abayes Single branch test method. Performs an approximate Bayes test. Can be used with other \'single branch test methods\' and ultrafast bootstrap. Values reported in the order of: alrt, lbp, abayes, ufboot. [default: False]" name="pabayes" selected="False" type="boolean" />
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|
410 <param label="--p-lbp: INTEGER Single branch test method. Number of bootstrap Range(1000, None) replicates to perform a fast local bootstrap probability method. Minimum of 1000 replicates is recomended. Can be used with other \'single branch test methods\'. Values reported in the order of: alrt, lbp, abayes, ufboot. [optional]" name="plbp" optional="False" type="text" />
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|
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411 <param label="--p-bnni: --p-bnni: / --p-no-bnni Optimize UFBoot trees by NNI on bootstrap alignment. This option reduces the risk of overestimating branch supports with UFBoot due to severe model violations. [default: False]" name="pbnni" selected="False" type="boolean" />
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412 <param label="--p-safe: --p-safe: / --p-no-safe Safe likelihood kernel to avoid numerical underflow. [default: False]" name="psafe" selected="False" type="boolean" />
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|
|
413 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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|
|
414
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|
415 </inputs>
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416
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|
417 <outputs>
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|
418 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
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419
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|
|
420 </outputs>
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|
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421
|
|
|
422 <help><![CDATA[
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|
|
423 Construct a phylogenetic tree with IQ-TREE with bootstrap supports.
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|
|
424 ###############################################################
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|
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425
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|
|
426 Construct a phylogenetic tree using IQ-TREE (http://www.iqtree.org/) with
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|
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427 automatic model selection and bootstrap supports.
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428
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|
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429 Parameters
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|
|
430 ----------
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|
|
431 alignment : FeatureData[AlignedSequence]
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|
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432 Aligned sequences to be used for phylogenetic reconstruction.
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|
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433 seed : Int, optional
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|
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434 Random number seed. If not set, program defaults will be used. See IQ-
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|
|
435 TREE manual for details.
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|
|
436 n_cores : Int % Range(1, None) | Str % Choices('auto'), optional
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|
|
437 The number of cores to use for parallel processing. Use `auto` to let
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|
|
438 IQ-TREE automatically determine the optimal number of cores to use.
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|
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439 n_cores_max : Int % Range(2, None), optional
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|
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440 Limits the maximum number of cores to be used when 'n_cores' is set to
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|
|
441 'auto'.
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|
|
442 n_runs : Int % Range(1, None), optional
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|
|
443 Number of indepedent runs. Multiple independent runs (e.g. 10) can
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|
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444 outperform a single run in terms of likelihood maximisation.
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|
|
445 substitution_model : Str % Choices('JC', 'JC+I', 'JC+G', 'JC+I+G', 'JC+R2', 'JC+R3', 'JC+R4', 'JC+R5', 'JC+R6', 'JC+R7', 'JC+R8', 'JC+R9', 'JC+R10', 'F81', 'F81+I', 'F81+G', 'F81+I+G', 'F81+R2', 'F81+R3', 'F81+R4', 'F81+R5', 'F81+R6', 'F81+R7', 'F81+R8', 'F81+R9', 'F81+R10', 'K80', 'K80+I', 'K80+G', 'K80+I+G', 'K80+R2', 'K80+R3', 'K80+R4', 'K80+R5', 'K80+R6', 'K80+R7', 'K80+R8', 'K80+R9', 'K80+R10', 'HKY', 'HKY+I', 'HKY+G', 'HKY+I+G', 'HKY+R2', 'HKY+R3', 'HKY+R4', 'HKY+R5', 'HKY+R6', 'HKY+R7', 'HKY+R8', 'HKY+R9', 'HKY+R10', 'TNe', 'TNe+I', 'TNe+G', 'TNe+I+G', 'TNe+R2', 'TNe+R3', 'TNe+R4', 'TNe+R5', 'TNe+R6', 'TNe+R7', 'TNe+R8', 'TNe+R9', 'TNe+R10', 'TN', 'TN+I', 'TN+G', 'TN+I+G', 'TN+R2', 'TN+R3', 'TN+R4', 'TN+R5', 'TN+R6', 'TN+R7', 'TN+R8', 'TN+R9', 'TN+R10', 'K81', 'K81+I', 'K81+G', 'K81+I+G', 'K81+R2', 'K81+R3', 'K81+R4', 'K81+R5', 'K81+R6', 'K81+R7', 'K81+R8', 'K81+R9', 'K81+R10', 'K81u', 'K81u+I', 'K81u+G', 'K81u+I+G', 'K81u+R2', 'K81u+R3', 'K81u+R4', 'K81u+R5', 'K81u+R6', 'K81u+R7', 'K81u+R8', 'K81u+R9', 'K81u+R10', 'TPM2', 'TPM2+I', 'TPM2+G', 'TPM2+I+G', 'TPM2+R2', 'TPM2+R3', 'TPM2+R4', 'TPM2+R5', 'TPM2+R6', 'TPM2+R7', 'TPM2+R8', 'TPM2+R9', 'TPM2+R10', 'TPM2u', 'TPM2u+I', 'TPM2u+G', 'TPM2u+I+G', 'TPM2u+R2', 'TPM2u+R3', 'TPM2u+R4', 'TPM2u+R5', 'TPM2u+R6', 'TPM2u+R7', 'TPM2u+R8', 'TPM2u+R9', 'TPM2u+R10', 'TPM3', 'TPM3+I', 'TPM3+G', 'TPM3+I+G', 'TPM3+R2', 'TPM3+R3', 'TPM3+R4', 'TPM3+R5', 'TPM3+R6', 'TPM3+R7', 'TPM3+R8', 'TPM3+R9', 'TPM3+R10', 'TPM3u', 'TPM3u+I', 'TPM3u+G', 'TPM3u+I+G', 'TPM3u+R2', 'TPM3u+R3', 'TPM3u+R4', 'TPM3u+R5', 'TPM3u+R6', 'TPM3u+R7', 'TPM3u+R8', 'TPM3u+R9', 'TPM3u+R10', 'TIMe', 'TIMe+I', 'TIMe+G', 'TIMe+I+G', 'TIMe+R2', 'TIMe+R3', 'TIMe+R4', 'TIMe+R5', 'TIMe+R6', 'TIMe+R7', 'TIMe+R8', 'TIMe+R9', 'TIMe+R10', 'TIM', 'TIM+I', 'TIM+G', 'TIM+I+G', 'TIM+R2', 'TIM+R3', 'TIM+R4', 'TIM+R5', 'TIM+R6', 'TIM+R7', 'TIM+R8', 'TIM+R9', 'TIM+R10', 'TIM2e', 'TIM2e+I', 'TIM2e+G', 'TIM2e+I+G', 'TIM2e+R2', 'TIM2e+R3', 'TIM2e+R4', 'TIM2e+R5', 'TIM2e+R6', 'TIM2e+R7', 'TIM2e+R8', 'TIM2e+R9', 'TIM2e+R10', 'TIM2', 'TIM2+I', 'TIM2+G', 'TIM2+I+G', 'TIM2+R2', 'TIM2+R3', 'TIM2+R4', 'TIM2+R5', 'TIM2+R6', 'TIM2+R7', 'TIM2+R8', 'TIM2+R9', 'TIM2+R10', 'TIM3e', 'TIM3e+I', 'TIM3e+G', 'TIM3e+I+G', 'TIM3e+R2', 'TIM3e+R3', 'TIM3e+R4', 'TIM3e+R5', 'TIM3e+R6', 'TIM3e+R7', 'TIM3e+R8', 'TIM3e+R9', 'TIM3e+R10', 'TIM3', 'TIM3+I', 'TIM3+G', 'TIM3+I+G', 'TIM3+R2', 'TIM3+R3', 'TIM3+R4', 'TIM3+R5', 'TIM3+R6', 'TIM3+R7', 'TIM3+R8', 'TIM3+R9', 'TIM3+R10', 'TVMe', 'TVMe+I', 'TVMe+G', 'TVMe+I+G', 'TVMe+R2', 'TVMe+R3', 'TVMe+R4', 'TVMe+R5', 'TVMe+R6', 'TVMe+R7', 'TVMe+R8', 'TVMe+R9', 'TVMe+R10', 'TVM', 'TVM+I', 'TVM+G', 'TVM+I+G', 'TVM+R2', 'TVM+R3', 'TVM+R4', 'TVM+R5', 'TVM+R6', 'TVM+R7', 'TVM+R8', 'TVM+R9', 'TVM+R10', 'SYM', 'SYM+I', 'SYM+G', 'SYM+I+G', 'SYM+R2', 'SYM+R3', 'SYM+R4', 'SYM+R5', 'SYM+R6', 'SYM+R7', 'SYM+R8', 'SYM+R9', 'SYM+R10', 'GTR', 'GTR+I', 'GTR+G', 'GTR+I+G', 'GTR+R2', 'GTR+R3', 'GTR+R4', 'GTR+R5', 'GTR+R6', 'GTR+R7', 'GTR+R8', 'GTR+R9', 'GTR+R10', 'MFP', 'TEST'), optional
|
|
|
446 Model of Nucleotide Substitution.If not provided, IQ-TREE will
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|
|
447 determine the best fit substitution model automatically.
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|
|
448 bootstrap_replicates : Int % Range(1000, None), optional
|
|
|
449 The number of bootstrap searches to perform. Minimum of 1000
|
|
|
450 recomended.
|
|
|
451 n_init_pars_trees : Int % Range(1, None), optional
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|
|
452 Number of initial parsimony trees. If not set, program defaults will be
|
|
|
453 used. See IQ-TREE manual for details.
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|
|
454 n_top_init_trees : Int % Range(1, None), optional
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|
|
455 Number of top initial trees. If not set, program defaults will be used.
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|
|
456 See IQ-TREE manual for details.
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|
|
457 n_best_retain_trees : Int % Range(1, None), optional
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|
|
458 Number of best trees retained during search. If not set, program
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|
|
459 defaults will be used. See IQ-TREE manual for details.
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|
|
460 stop_iter : Int % Range(1, None), optional
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|
|
461 Number of unsuccessful iterations to stop. If not set, program defaults
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|
|
462 will be used. See IQ-TREE manual for details.
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|
|
463 perturb_nni_strength : Float % Range(0.01, 1.0), optional
|
|
|
464 Perturbation strength for randomized NNI. If not set, program defaults
|
|
|
465 will be used. See IQ-TREE manual for details.
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|
|
466 spr_radius : Int % Range(1, None), optional
|
|
|
467 Radius for parsimony SPR search. If not set, program defaults will be
|
|
|
468 used. See IQ-TREE manual for details.
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|
|
469 n_max_ufboot_iter : Int % Range(1, None), optional
|
|
|
470 Maximum number of iterations. If not set, program defaults will be
|
|
|
471 used. See IQ-TREE manual for details.
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|
|
472 n_ufboot_steps : Int % Range(1, None), optional
|
|
|
473 Number of iterations for UFBoot stopping rule. If not set, program
|
|
|
474 defaults will be used.See IQ-TREE manual for details.
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|
|
475 min_cor_ufboot : Float % Range(0.51, 0.99), optional
|
|
|
476 Minimum correlation coefficient. If not set, program defaults will be
|
|
|
477 used.See IQ-TREE manual for details.
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|
|
478 ep_break_ufboot : Float % Range(0.01, 0.99), optional
|
|
|
479 Epsilon value to break tie. If not set, program defaults will be used.
|
|
|
480 See IQ-TREE manual for details.
|
|
|
481 allnni : Bool, optional
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|
|
482 Perform more thorough NNI search.
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|
|
483 alrt : Int % Range(1000, None), optional
|
|
|
484 Single branch test method. Number of bootstrap replicates to perform an
|
|
|
485 SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000
|
|
|
486 replicates is recomended. Can be used with other 'single branch test
|
|
|
487 methods'. Values reported in the order of: alrt, lbp, abayes.
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|
|
488 abayes : Bool, optional
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|
|
489 Single branch test method. Performs an approximate Bayes test. Can be
|
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490 used with other 'single branch test methods' and ultrafast bootstrap.
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|
|
491 Values reported in the order of: alrt, lbp, abayes, ufboot.
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|
|
492 lbp : Int % Range(1000, None), optional
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|
|
493 Single branch test method. Number of bootstrap replicates to perform a
|
|
|
494 fast local bootstrap probability method. Minimum of 1000 replicates is
|
|
|
495 recomended. Can be used with other 'single branch test methods'. Values
|
|
|
496 reported in the order of: alrt, lbp, abayes, ufboot.
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|
|
497 bnni : Bool, optional
|
|
|
498 Optimize UFBoot trees by NNI on bootstrap alignment. This option
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499 reduces the risk of overestimating branch supports with UFBoot due to
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500 severe model violations.
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501 safe : Bool, optional
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502 Safe likelihood kernel to avoid numerical underflow.
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503
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504 Returns
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505 -------
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506 tree : Phylogeny[Unrooted]
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507 The resulting phylogenetic tree.
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508 ]]></help>
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509 <macros>
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510 <import>qiime_citation.xml</import>
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511 </macros>
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512 <expand macro="qiime_citation"/>
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513 </tool> |
