Mercurial > repos > iuc > hyphy_meme

annotate hyphy_meme.xml @ 35:7852b50fabb7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
author iuc
date Tue, 07 Oct 2025 20:48:02 +0000
parents 5fd8dc04d6af
children
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5fd8dc04d6af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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1 <tool id="hyphy_meme" name="HyPhy-MEME" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Mixed Effects Model of Evolution</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 @SYMLINK_FILES@
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10 @HYPHYMPI@ meme
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11 --alignment ./$input_file
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12 @INPUT_TREE@
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13 --code '$gencodeid'
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14 @branch_options@
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15 --pvalue '$p_value'
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16 --resample $resample
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17 --rates $rates
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18 --multiple-hits $multiple_hits_conditional.multiple_hits
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19 #if $multiple_hits_conditional.multiple_hits != "None":
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20 --site-multihit $multiple_hits_conditional.site_multihit
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21 #end if
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22 --impute-states '$impute_states'
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23 --precision $precision
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24 --kill-zero-lengths $kill_zero_lengths
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25 #if $restrict_sites_conditional.restrict_sites_flag == "true":
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26 --limit-to-sites '$restrict_sites_conditional.limit_to_sites'
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27 --save-lf-for-sites '$restrict_sites_conditional.save_lf_for_sites'
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28 #end if
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29 --output '$meme_output'
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30 --full-model '$full_model'
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31 > meme_stdout.md
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32 @ERRORS@
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33 ]]></command>
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34 <inputs>
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35 <expand macro="inputs"/>
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36 <expand macro="gencode"/>
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37 <expand macro="branches"/>
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38 <param argument="--pvalue" name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/>
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39 <section name="advanced_options" title="Advanced Options" expanded="false">
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40 <expand macro="resample"/>
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41 <param argument="--rates" type="integer" value="2" min="2" max="4" label="Number of omega rate classes"/>
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42 <conditional name="multiple_hits_conditional">
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43 <param argument="--multiple-hits" type="select" label="Include support for multiple nucleotide substitutions">
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44 <option value="Double">Include branch-specific rates for double nucleotide substitutions</option>
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45 <option value="Double+Triple">Include branch-specific rates for double and triple nucleotide substitutions</option>
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46 <option value="None" selected="true">Use standard models which permit only single nucleotide changes to occur instantly</option>
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47 </param>
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48 <when value="Double">
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49 <param argument="--site-multihit" type="select" label="Estimate multiple hit rates for each site">
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50 <option value="Estimate" selected="true">Estimate</option>
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51 <option value="No">No</option>
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52 </param>
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53 </when>
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54 <when value="Double+Triple">
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55 <param argument="--site-multihit" type="select" label="Estimate multiple hit rates for each site">
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56 <option value="Estimate" selected="true">Estimate</option>
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57 <option value="No">No</option>
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58 </param>
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59 </when>
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60 <when value="None">
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61 </when>
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62 </conditional>
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63 <param argument="--impute-states" type="boolean" truevalue="Yes" falsevalue="No" label="Impute likely character states for each sequence"/>
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64 <param argument="--precision" type="select" label="Optimization precision for preliminary fits">
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65 <option value="standard">Standard</option>
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66 <option value="reduced">Reduced for faster fitting</option>
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67 </param>
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68 <expand macro="kill_zero_lengths_param"/>
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69 <conditional name="restrict_sites_conditional">
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70 <param name="restrict_sites_flag" type="select" label="Restrict MEME analysis to a subset of sites" help="If Yes, allows specifying a subset of sites for analysis.">
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71 <option value="true">Yes</option>
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72 <option value="false" selected="true">No</option>
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73 </param>
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74 <when value="true">
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75 <param argument="--limit-to-sites" type="text" optional="true" label="Only analyze sites whose 1-based indices match the following list (null to skip)" help="Comma-separated list of site indices."/>
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76 <param argument="--save-lf-for-sites" type="text" optional="true" label="For sites whose 1-based indices match the following list, write out likelihood function snapshots (empty string to skip)" help="Comma-separated list of site indices."/>
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77 </when>
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78 <when value="false">
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79 </when>
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80 </conditional>
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81 <param argument="--full-model" type="boolean" truevalue="Yes" falsevalue="No" checked="true" label="Perform branch length re-optimization under the full codon model" />
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82 </section>
0
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83 </inputs>
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84 <outputs>
2
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85 <data name="meme_output" format="hyphy_results.json" />
35
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86 <data name="meme_md_report" format="markdown" from_work_dir="meme_stdout.md" label="MEME Report (Markdown) for ${tool.name} on ${on_string}" />
0
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87 </outputs>
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88 <tests>
35
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89 <test expect_num_outputs="2">
0
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90 <param name="input_file" ftype="fasta" value="meme-in1.fa"/>
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91 <param name="input_nhx" ftype="nhx" value="meme-in1.nhx"/>
31
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92 <conditional name="branch_cond">
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93 <param name="branch_sel" value="All"/>
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94 </conditional>
0
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95 <param name="p_value" value="0.1"/>
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96 <output name="meme_output">
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97 <assert_contents>
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98 <has_text text="fits"/>
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99 <has_text text="branch attributes"/>
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100 <has_text text="Global MG94xREV"/>
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101 </assert_contents>
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102 </output>
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103 <output name="meme_md_report">
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104 <assert_contents>
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105 <has_text text="### For partition 1 these sites are significant at p &lt;=0.1"/>
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106 </assert_contents>
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107 </output>
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108 </test>
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109 <test expect_num_outputs="2">
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110 <param name="input_file" ftype="fasta" value="meme-in1.fa"/>
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111 <param name="input_nhx" ftype="nhx" value="meme-in1.nhx"/>
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112 <conditional name="branch_cond">
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113 <param name="branch_sel" value="Internal"/>
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114 </conditional>
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115 <section name="advanced_options">
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116 <param name="rates" value="3"/>
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117 </section>
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118 <output name="meme_output">
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119 <assert_contents>
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120 <has_text text="fits"/>
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121 <has_text text="branch attributes"/>
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122 <has_text text="Mixture distribution weight allocated to negative/neutral evolution component 2"/>
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123 </assert_contents>
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124 </output>
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125 <output name="meme_md_report">
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126 <assert_contents>
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127 <has_text text=">rates => 3"/>
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128 <has_text text="non-syn rate (beta) distribution, rates : weights"/>
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129 </assert_contents>
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130 </output>
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131 </test>
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132 <test expect_num_outputs="2">
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133 <param name="input_file" ftype="fasta" value="meme-in1.fa"/>
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134 <param name="input_nhx" ftype="nhx" value="meme-in1.nhx"/>
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135 <section name="advanced_options">
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136 <param name="impute_states" value="Yes"/>
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137 <conditional name="multiple_hits_conditional">
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138 <param name="multiple_hits" value="Double"/>
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139 </conditional>
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140 </section>
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141
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142 <output name="meme_output">
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143 <assert_contents>
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144 <has_text text="fits"/>
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145 <has_text text="Imputed States"/>
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146 <has_text text="Relative rate estimate for 2-nucleotide substitutions"/>
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147 </assert_contents>
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148 </output>
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149 <output name="meme_md_report">
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150 <assert_contents>
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151 <has_text text="rate at which 2 nucleotides are changed instantly within a single codon"/>
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152 </assert_contents>
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153 </output>
0
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154 </test>
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155 </tests>
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156 <help><![CDATA[
5
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157 MEME: Mixed Effects Model of Evolution
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158 ======================================
8
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159
35
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160 **What question does this method answer?**
5
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161
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162 Which site(s) in a gene are subject to pervasive or *episodic*, i.e. only on a
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163 single lineage or subset of lineages, diversifying selection?
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164
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165 **Recommended Applications**
5
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166
8
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167 The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics
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168 (or balancing selection), including adaptive immune escape by viruses.
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169 MEME is ideally suited to identify sites under positive selection which
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170 represent candidate sites subject to strong selective pressures across the entire phylogeny or only on parts of the phylogeny.
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171
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172 MEME is the sole method in HyPhy for detecting selection at individual sites that considers both pervasive and episodic selection.
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173 MEME is therefore our recommended method if maximum power is desired.
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174
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175 **Methodology**
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176
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177 MEME (Mixed Effects Model of Evolution) is a powerful statistical method for detecting sites in a coding alignment that have been subject to positive selection. It extends classical fixed-effects likelihood (FEL) models by allowing the non-synonymous substitution rate (dN) to vary from branch to branch at a given site. This "mixed-effects" approach provides increased power to detect episodic selection, where a site may be under positive selection in some lineages but under neutral or purifying selection in others.
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178
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179 **The Intuition**
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180
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181 Imagine you are studying the evolution of a gene across a group of species. Some sites in that gene might be under constant pressure to change (pervasive selection), while others might only experience this pressure for a short period of time in a specific lineage (episodic selection). For example, a virus might evolve a new protein to escape the host's immune system, but once the host population adapts, the pressure on that protein might disappear.
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182
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183 Standard methods that assume a single dN/dS rate across the entire phylogeny might miss this kind of episodic selection. MEME addresses this by modeling the dN/dS ratio at each site as a mixture of two or more rate classes. For each site, MEME infers the probability that it evolves under each rate class on a given branch. This allows the model to identify sites that show evidence of positive selection (dN/dS > 1) even if that selection is confined to a small number of lineages.
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184
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185 **The Test**
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186
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187 For each site, MEME fits a baseline model where dN/dS is constrained to be less than or equal to 1, and an alternative model where a proportion of branches are allowed to have a dN/dS ratio greater than 1. A likelihood ratio test (LRT) is then used to determine if the alternative model provides a significantly better fit to the data. A significant p-value indicates that the site has experienced episodic diversifying selection.
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188
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189 **Input**
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190
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191 1. A *FASTA* sequence alignment.
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192 2. A phylogenetic tree in the *Newick* format
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193
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194 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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195
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196
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197 **Output**
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198
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199 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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200
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201 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/MEME for an example)
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202
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203 **Further reading**
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204
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205 http://hyphy.org/methods/selection-methods/#MEME
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206
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207
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208 **Tool options**
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209 ::
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210
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211 --alignment [required] An in-frame codon alignment in one of the formats supported by HyPhy.
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212 --tree [conditionally required] A phylogenetic tree (optionally annotated with {}).
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213
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214 --code Which genetic code to use (see tool form for available options).
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215
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216 --branches Which branches should be tested for selection?
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217 All [default] : test all branches.
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218 Internal : test only internal branches (suitable for intra-host pathogen evolution for example, where terminal branches may contain polymorphism data).
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219 Leaves: test only terminal (leaf) branches.
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220 Unlabeled: if the Newick string is labeled using the {} notation, test only branches without explicit labels (see http://hyphy.org/tutorials/phylotree/).
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221 Custom : Enter a branch label.
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222
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223 --pvalue The significance level used to determine significance (default: 0.1, range: 0 to 1).
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224
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225 --resample Perform parametric bootstrap resampling to derive site-level null LRT distributions.
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226 Warning: This will result in a significantly slower analysis. A value of 0 means no resampling is performed. This parameter specifies the maximum number of replicates per site (default: 0, range: 0 to 1000).
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227
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228 --rates The number omega rate classes to include in the model (default: 2, range: 2 to 4).
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229
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230 --multiple-hits Include support for multiple nucleotide substitutions.
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231 Double : Include branch-specific rates for double nucleotide substitutions.
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232 Double+Triple : Include branch-specific rates for double and triple nucleotide substitutions.
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233 None [default] : Use standard models which permit only single nucleotide changes to occur instantly.
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234
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235 --site-multihit Estimate multiple hit rates for each site. This option is available only if 'Include support for multiple nucleotide substitutions' is set to 'Double' or 'Double+Triple'.
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236 Estimate [default] : Estimate multiple hit rates.
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237 No : Do not estimate multiple hit rates.
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238
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239 --impute-states Use site-level model fits to impute likely character states for each sequence (default: No).
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240
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241 --precision Optimization precision settings for preliminary fits.
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242 Standard [default]
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243 Reduced for faster fitting
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244
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245 --kill-zero-lengths Automatically delete internal zero-length branches for computational efficiency.
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246 Yes [default] : Automatically delete internal zero-length branches for computational efficiency (will not affect results otherwise).
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247 Constrain : Keep zero-length branches, but constrain their values to 0.
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248 No : Keep all branches.
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249
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250 --restrict-sites Restrict MEME analysis to a subset of sites. If Yes, allows specifying a subset of sites for analysis.
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251 Yes : Restrict analysis to a subset of sites.
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252 No [default] : Do not restrict analysis to a subset of sites.
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253
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254 --limit-to-sites Only analyze sites whose 1-based indices match the following list (null to skip). This option is available only if 'Restrict MEME analysis to a subset of sites' is set to 'Yes'. Comma-separated list of site indices.
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255 --save-lf-for-sites For sites whose 1-based indices match the following list, write out likelihood function snapshots (empty string to skip). This option is available only if 'Restrict MEME analysis to a subset of sites' is set to 'Yes'. Comma-separated list of site indices.
7852b50fabb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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256
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257 --full-model Perform branch length re-optimization under the full codon model (default: Yes).
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258
0
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259 ]]></help>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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260 <expand macro="citations">
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261 <citation type="doi">10.1371/journal.pgen.1002764</citation>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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262 </expand>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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263 </tool>