Mercurial > repos > iuc > hyphy_fel

annotate hyphy_fel.xml @ 36:ef2129a50a13 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 20:45:18 +0000
parents ec783806a5c3
children
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1 <tool id="hyphy_fel" name="HyPhy-FEL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Fixed Effects Likelihood</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 @SHELL_OPTIONS@
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11 @HYPHYMPI@ fel
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12 --alignment ./$input_file
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13 @INPUT_TREE@
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14 --code '$gencodeid'
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15 --multiple-hits $multiple_hits_conditional.multiple_hits
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16 @branch_options@
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17 --srv '$include_srv'
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18 --pvalue '$p_value'
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19 @resample@
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20 #if $restrict_sites_conditional.restrict_sites_flag == "true":
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21 --limit-to-sites '$restrict_sites_conditional.limit_to_sites'
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22 --save-lf-for-sites '$restrict_sites_conditional.save_lf_for_sites'
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23 #end if
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24 --precision $precision
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25 $ci
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26 --output '$fel_output'
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27 #if $multiple_hits_conditional.multiple_hits != "None":
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28 --site-multihit $multiple_hits_conditional.site_multihit
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29 #end if
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30
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31 --kill-zero-lengths $kill_zero_lengths
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32 #if $full_model:
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33 --full-model $full_model
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34 #end if
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35 > fel_stdout.md
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36 @ERRORS@
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37 ]]></command>
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38 <inputs>
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39 <expand macro="inputs"/>
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40 <expand macro="gencode"/>
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41 <expand macro="branches"/>
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42 <param argument="--pvalue" name="p_value" type="float" value=".1" min="0" max="1" label="P-value"/>
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43 <section name="advanced_options" title="Advanced Options" expanded="false">
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44 <param name="include_srv" type="select" label="Include synonymous rate variation" help = "Allow synonymous rates to vary from site to site">
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45 <option value="Yes">Yes (recommended)</option>
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46 <option value="No">No</option>
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47 </param>
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48 <conditional name="multiple_hits_conditional">
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49 <param argument="--multiple-hits" type="select" label="Include support for multiple nucleotide substitutions">
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50 <option value="Double">Include branch-specific rates for double nucleotide substitutions</option>
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51 <option value="Double+Triple">Include branch-specific rates for double and triple nucleotide substitutions</option>
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52 <option value="None" selected="true">Use standard models which permit only single nucleotide changes to occur instantly</option>
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53 </param>
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54 <when value="Double">
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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="Double+Triple">
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61 <param argument="--site-multihit" type="select" label="Estimate multiple hit rates for each site">
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62 <option value="Estimate" selected="true">Estimate</option>
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63 <option value="No">No</option>
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64 </param>
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65 </when>
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66 <when value="None">
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67 </when>
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68 </conditional>
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69 <param argument="--ci" type="boolean" truevalue="--ci Yes" falsevalue="" label="Compute profile likelihood confidence intervals for each variable site" />
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70 <expand macro="resample"/>
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71 <conditional name="restrict_sites_conditional">
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72 <param name="restrict_sites_flag" type="select" label="Restrict FEL analysis to a subset of sites" help="If Yes, allows specifying a subset of sites for analysis.">
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73 <option value="true">Yes</option>
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74 <option value="false" selected="true">No</option>
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75 </param>
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76 <when value="true">
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77 <param argument="--limit-to-sites" type="text" optional="true" label="Only analyze sites whose 1-based indices match the following list (null to skip)" value="null" help="Comma-separated list of site indices."/>
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78 <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 (null to skip)" value="null" help="Comma-separated list of site indices."/>
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79 </when>
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80 <when value="false">
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81 </when>
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82 </conditional>
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83 <param argument="--precision" type="select" label="Optimization precision for preliminary fits">
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84 <option value="standard">Standard</option>
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85 <option value="reduced">Reduced for faster fitting</option>
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86 </param>
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87
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88 <expand macro="kill_zero_lengths_param"/>
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89 <param argument="--full-model" type="boolean" truevalue="Yes" falsevalue="No" checked="true" label="Perform branch length re-optimization under the full codon model" help="If true, re-optimizes branch lengths under the full codon model."/>
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90 </section>
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91
0
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92 </inputs>
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93 <outputs>
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94 <data name="fel_md_report" format="markdown" from_work_dir="fel_stdout.md" label="FEL Report (Markdown) for ${tool.name} on ${on_string}" />
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95 <data name="fel_output" format="hyphy_results.json" />
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96
0
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97 </outputs>
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98 <tests>
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99 <test expect_num_outputs="2">
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100 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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101 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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102 <output name="fel_output">
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103 <assert_contents>
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104 <has_text text="Likelihood ratio test statistic for beta = alpha, versus beta " />
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105 </assert_contents>
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106 </output>
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107 <output name="fel_md_report">
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108 <assert_contents>
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109 <has_text text="sites under pervasive positive diversifying and" />
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110 </assert_contents>
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111 </output>
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112 </test>
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113 <test expect_num_outputs="2">
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114 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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115 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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116 <param name="advanced_options|ci" value="true" />
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117 <param name="advanced_options|precision" value="reduced" />
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118 <param name="p_value" value="0.05" />
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119 <output name="fel_output">
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120 <assert_contents>
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121 <has_text text="Likelihood ratio test statistic for beta = alpha, versus beta " />
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122 <has_text text="95% profile likelihood CI upper bound for dN/dS (if available)" />
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123 </assert_contents>
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124 </output>
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125 <output name="fel_md_report">
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126 <assert_contents>
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127 <has_text text="sites under pervasive positive diversifying and" />
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128 <has_text text=">precision => reduced" />
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129 <has_text text="### For partition 1 these sites are significant at p &lt;=0.05" />
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130 </assert_contents>
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131 </output>
0
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132 </test>
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133 <test expect_num_outputs="2">
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134 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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135 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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136 <section name="advanced_options">
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137 <conditional name="restrict_sites_conditional">
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138 <param name="restrict_sites_flag" value="true" />
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139 <param name="limit_to_sites" value="1,2,3" />
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140 </conditional>
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141 </section>
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142 <output name="fel_output">
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143 <assert_contents>
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144 <has_text text="&quot;site-filter&quot;:&quot;1,2,3&quot;" />
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145 <has_text text="Likelihood ratio test statistic for beta = alpha, versus beta " />
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146 </assert_contents>
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147 </output>
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148 <output name="fel_md_report">
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149 <assert_contents>
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150 <has_text text=">limit-to-sites => 1,2,3" />
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151 <has_text text="sites under pervasive positive diversifying and" />
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152 </assert_contents>
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153 </output>
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154 </test>
0
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155 </tests>
1
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156 <help><![CDATA[
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157 FEL : Fixed effects likelihood
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158 ==============================
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159
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160 What question does this method answer?
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161 --------------------------------------
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162
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163 FEL (Fixed Effects Likelihood) is a statistical method used to identify individual sites in a gene that are subject to pervasive diversifying selection. It addresses the question: Which specific sites in a gene show evidence of positive selection that has been consistently maintained across the entire evolutionary phylogeny of the analyzed sequences?
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164
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165 Recommended Applications
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166 ------------------------
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167
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168 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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169 (or balancing selection), including adaptive immune escape by viruses. As such, FEL 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.
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171
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172 FEL is our recommended method for analyzing small-to-medium size datasets when one wishes only to study pervasive selection at individual sites.
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173
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174 Brief description
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175 -----------------
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176
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177 FEL (Fixed Effects Likelihood) is a powerful method for detecting pervasive positive or negative selection at individual sites in a coding sequence. It operates by estimating site-wise synonymous (alpha, dS) and non-synonymous (beta, dN) substitution rates using a maximum likelihood approach. For each site, FEL then performs a likelihood ratio test (LRT) to compare a null model (where dN = dS) against an alternative model (where dN != dS). A significant p-value from this test indicates that the site is under selection. The method aggregates information across all branches of the phylogenetic tree, making it suitable for identifying sites under pervasive diversifying selection (dN > dS) or pervasive purifying selection (dN < dS). While primarily designed for pervasive selection, FEL can also infer an additional nuisance parameter for the non-synonymous rate on branches not selected for testing, allowing for analysis of a subset of branches.
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178
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179 **Intuition:** Imagine you're looking at a gene's evolution across different species. Some parts of the gene might change a lot (diversifying selection), while others stay the same (purifying selection). FEL helps pinpoint the exact "letters" (sites) in the gene that are consistently under pressure to change or stay the same throughout its evolutionary history. It does this by comparing how often synonymous (silent) changes happen versus non-synonymous (amino acid altering) changes at each site. If non-synonymous changes happen significantly more often, it suggests positive selection.
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180
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181
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182 Input
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183 -----
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184
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185 1. A *FASTA* sequence alignment.
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186 2. A phylogenetic tree in the *Newick* format
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187
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188 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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189
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190
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191 Output
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192 ------
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193
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194 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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195 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/FEL for an example)
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196
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197 Further reading
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198 ---------------
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199
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200 http://hyphy.org/methods/selection-methods/#FEL
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201
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202
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203 Tool options
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204 ------------
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205 ::
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206
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207 --alignment [required] An in-frame codon alignment in one of the formats supported by HyPhy.
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208 --tree [conditionally required] A phylogenetic tree (optionally annotated with {}).
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209
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210 --code Which genetic code to use (see tool form for available options).
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211
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212 --multiple-hits Include support for multiple nucleotide substitutions.
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213 Double : Include branch-specific rates for double nucleotide substitutions.
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214 Double+Triple : Include branch-specific rates for double and triple nucleotide substitutions.
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215 None [default] : Use standard models which permit only single nucleotide changes to occur instantly.
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216
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217 --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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218 Estimate [default] : Estimate multiple hit rates.
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219 No : Do not estimate multiple hit rates.
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220
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221 --branches Which branches should be tested for selection?
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222 All [default] : test all branches.
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223 Internal : test only internal branches (suitable for intra-host pathogen evolution for example, where terminal branches may contain polymorphism data).
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224 Leaves: test only terminal (leaf) branches.
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225 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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226 Custom : Enter a branch label.
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227
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228 --pvalue The significance level used to determine significance (default: 0.1, range: 0 to 1).
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229
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230 --srv Include site-to-site synonymous rate variation?
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231 Yes [default] : Allow synonymous rates to vary from site to site.
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232 No : Do not allow synonymous rates to vary.
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233
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234 --ci Compute profile likelihood confidence intervals for each variable site (default: No).
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235
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236 Advanced Attributes
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237 -------------------
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238 ::
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239
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240 --resample Perform parametric bootstrap resampling to derive site-level null LRT distributions.
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241 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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242
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243 --restrict-sites Restrict FEL analysis to a subset of sites. If Yes, allows specifying a subset of sites for analysis.
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244 Yes : Restrict analysis to a subset of sites.
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245 No [default] : Do not restrict analysis to a subset of sites.
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246
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247 --limit-to-sites Only analyze sites whose 1-based indices match the following list (null to skip). This option is available only if 'Restrict FEL analysis to a subset of sites' is set to 'Yes'. Comma-separated list of site indices.
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248 --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 FEL analysis to a subset of sites' is set to 'Yes'. Comma-separated list of site indices.
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249
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250 --precision Optimization precision settings for preliminary fits.
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251 Standard [default]
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252 Reduced for faster fitting
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253
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254 --kill-zero-lengths Automatically delete internal zero-length branches for computational efficiency.
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255 Yes [default] : Automatically delete internal zero-length branches for computational efficiency (will not affect results otherwise).
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256 Constrain : Keep zero-length branches, but constrain their values to 0.
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257 No : Keep all branches.
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258
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259 --full-model Perform branch length re-optimization under the full codon model (default: Yes). If true, re-optimizes branch lengths under the full codon model.
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260
ef2129a50a13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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261 ]]>;
ef2129a50a13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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262 </help>
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263
0
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264 <expand macro="citations">
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265 <citation type="doi">10.1093/molbev/msi105</citation>
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266 </expand>
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267 </tool>