annotate phylogenetic_tree.xml @ 32:03c22b722882

remove BeautifulSoup dependency
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 20 Sep 2013 13:54:23 -0400
parents a631c2f6d913
children
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1 <tool id="gd_phylogenetic_tree" name="Phylogenetic Tree" version="1.1.0">
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2 <description>: Show genetic relationships among individuals</description>
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3
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4 <command interpreter="python">
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5 #import json
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6 #import base64
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7 #import zlib
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8 #set $ind_names = $input.dataset.metadata.individual_names
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9 #set $ind_colms = $input.dataset.metadata.individual_columns
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10 #set $ind_dict = dict(zip($ind_names, $ind_colms))
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11 #set $ind_json = json.dumps($ind_dict, separators=(',',':'))
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12 #set $ind_comp = zlib.compress($ind_json, 9)
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13 #set $ind_arg = base64.b64encode($ind_comp)
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14 phylogenetic_tree.py '$input' '$output' '$output.files_path'
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15 #if $input_type.choice == '0'
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16 'gd_snp'
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17 #if $input_type.data_source.choice == '0'
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18 'sequence_coverage'
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19 '$input_type.data_source.minimum_coverage'
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20 '$input_type.data_source.minimum_quality'
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21 #else if $input_type.data_source.choice == '1'
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22 'estimated_genotype' '0' '0'
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23 #end if
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24 #else if $input_type.choice == '1'
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25 'gd_genotype' 'estimated_genotype' '0' '0'
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26 #end if
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27 #if $individuals.choice == '0'
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28 'all_individuals'
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29 #else if $individuals.choice == '1'
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30 '$individuals.p1_input'
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31 #end if
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32 #if ((str($input.metadata.scaffold) == str($input.metadata.ref)) and (str($input.metadata.pos) == str($input.metadata.rPos))) or (str($include_reference) == '0')
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33 'none'
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34 #else
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35 '$input.metadata.dbkey'
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36 #end if
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37 #set $draw_tree_options = ''.join(str(x) for x in [$branch_style, $scale_style, $length_style, $layout_style])
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38 #if $draw_tree_options == ''
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39 ''
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40 #else
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41 '-$draw_tree_options'
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42 #end if
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43 '$ind_arg'
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44 </command>
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45
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46 <inputs>
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47 <conditional name="input_type">
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48 <param name="choice" type="select" format="integer" label="Input format">
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49 <option value="0" selected="true">gd_snp</option>
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50 <option value="1">gd_genotype</option>
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51 </param>
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52 <when value="0">
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53 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
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54
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55 <conditional name="data_source">
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56 <param name="choice" type="select" format="integer" label="Distance metric">
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57 <option value="0">sequence coverage</option>
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58 <option value="1" selected="true">estimated genotype</option>
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59 </param>
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60 <when value="0">
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61 <param name="minimum_coverage" type="integer" min="0" value="0" label="Minimum SNP coverage" />
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62 <param name="minimum_quality" type="integer" min="0" value="0" label="Minimum SNP quality"
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63 help="Note: minimum coverage and minimum quality cannot both be 0" />
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64 </when>
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65 <when value="1"/>
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66 </conditional>
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67 </when>
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68 <when value="1">
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69 <param name="input" type="data" format="gd_genotype" label="Genotype dataset" />
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70 </when>
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71 </conditional>
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72
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73 <conditional name="individuals">
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74 <param name="choice" type="select" label="Compute for">
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75 <option value="0" selected="true">All individuals</option>
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76 <option value="1">Individuals in a population</option>
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77 </param>
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78 <when value="0" />
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79 <when value="1">
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80 <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" />
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81 </when>
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82 </conditional>
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83
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84 <param name="include_reference" type="select" format="integer" label="Include reference sequence">
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85 <option value="1" selected="true">Yes</option>
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86 <option value="0">No</option>
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87 </param>
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88
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89 <param name="branch_style" type="select" display="radio">
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90 <label>Branch type</label>
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91 <option value="" selected="true">square</option>
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92 <option value="d">diagonal</option>
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93 </param>
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94
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95 <param name="scale_style" type="select" display="radio">
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96 <label>Draw branches to scale</label>
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97 <option value="" selected="true">yes</option>
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98 <option value="s">no</option>
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99 </param>
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100
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101 <param name="length_style" type="select" display="radio">
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102 <label>Show branch lengths</label>
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103 <option value="" selected="true">yes</option>
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104 <option value="b">no</option>
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105 </param>
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106
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107 <param name="layout_style" type="select" display="radio">
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108 <label>Tree layout</label>
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109 <option value="" selected="true">horizontal</option>
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110 <option value="v">vertical</option>
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111 </param>
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112 </inputs>
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113
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114 <outputs>
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115 <data name="output" format="html" />
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116 </outputs>
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117
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118 <tests>
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119 <test>
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120 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
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121 <param name="choice" value="0" />
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122 <param name="minimum_coverage" value="3" />
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123 <param name="minimum_quality" value="30" />
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124 <param name="data_source" value="0" />
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125 <param name="branch_style" value="" />
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126 <param name="scale_style" value="" />
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127 <param name="length_style" value="" />
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128 <param name="layout_style" value="" />
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129 <output name="output" file="test_out/phylogenetic_tree/phylogenetic_tree.html" ftype="html" compare="diff" lines_diff="2">
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130 <extra_files type="file" name="distance_matrix.phylip" value="test_out/phylogenetic_tree/distance_matrix.phylip" />
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131 <extra_files type="file" name="informative_snps.txt" value="test_out/phylogenetic_tree/informative_snps.txt" />
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132 <extra_files type="file" name="mega_distance_matrix.txt" value="test_out/phylogenetic_tree/mega_distance_matrix.txt" />
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133 <extra_files type="file" name="phylogenetic_tree.newick" value="test_out/phylogenetic_tree/phylogenetic_tree.newick" />
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134 <extra_files type="file" name="tree.pdf" value="test_out/phylogenetic_tree/tree.pdf" compare="sim_size" delta = "1000"/>
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135 </output>
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136 </test>
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137 </tests>
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138
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139 <requirements>
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140 <requirement type="package" version="1.3">phast</requirement>
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141 <requirement type="package" version="1.1">quicktree</requirement>
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142 <requirement type="package" version="0.1">gd_c_tools</requirement>
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143 </requirements>
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144
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145
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146 <help>
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147
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148 **Dataset formats**
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149
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150 The input dataset is in gd_snp_ or gd_genotype_ format.
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151 The output is a composite dataset, containing the tree in both text (Newick_)
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152 and PostScript formats, as well as supplemental text information.
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153 (`Dataset missing?`_)
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154
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155 .. _gd_snp: ./static/formatHelp.html#gd_snp
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156 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
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157 .. _Newick: http://evolution.genetics.washington.edu/phylip/newicktree.html
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158 .. _Dataset missing?: ./static/formatHelp.html
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159
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160 -----
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161
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162 **What it does**
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163
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164 This tool uses a gd_snp dataset to determine a kind of "genetic distance"
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165 between each pair of individuals. That information is used to
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166 produce a tree-shaped figure that depicts how the individuals are related,
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167 both as a text files and as a diagram.
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168 The text files include a common tree format, Newick, as well as distance
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169 matrices and counts of informative SNPs for each pairwise comparison.
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170 The informative SNPs can be used as a guide to how reliable the tree is.
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171
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172 The input parameters are:
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173
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174 SNP dataset
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175 A table of SNPs for various individuals, in gd_snp format.
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176
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177 Individuals
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178 By default all individuals are included in the analysis, but this can
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179 optionally be restricted to a subset that has been defined using the
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180 Specify Individuals tool.
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181
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182 Minimum SNP coverage
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183 For each pair of individuals, the tool looks for informative SNPs, i.e.,
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184 where the sequence data for both individuals is adequate. Specifying,
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185 say, 7 for this option instructs the tool to consider only SNPs with
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186 at least 7 reads in each of the two individuals (regardless of the
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187 alleles) when estimating their genetic distance.
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188
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189 Minimum SNP quality
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190 Specifying, say, 37 for this option instructs the tool to consider
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191 only SNPs with a quality score of at least 37 in both individuals
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192 when estimating their genetic distance.
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193
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194 Include reference sequence
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195 For gd_snp datasets containing columns for a reference sequence, the
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196 user can ask that the reference be indicated in the tree, to help with
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197 rooting it. If the dataset has no reference columns, this option has
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198 no effect.
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199
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200 Distance metric
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201 The genetic distance between two individuals at a given SNP can
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202 be estimated two ways. One method is to use the absolute value of the
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203 difference in the frequency of the first allele (or equivalently, the
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204 second allele). For instance, if the first individual has 5 reads of
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205 each allele and the second individual has respectively 3 and 6 reads,
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206 then the frequencies are 1/2 and 1/3, giving a distance 1/6 at that
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207 SNP. The other approach is to use the genotype calls to estimate
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208 the difference in the number of occurrences of the first allele.
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209 For instance, if the two genotypes are 2 and 1, i.e., the individuals
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210 are estimated to have respectively 2 and 1 occurrences of the first
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211 allele at this location, then the distance is 1 (the absolute value
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212 of the difference of the two numbers).
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213
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214 Output options
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215 The final four options apply mostly to the graphical drawing of the
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216 tree, except that the branch lengths are also added to the Newick text
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217 file.
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218
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219 -----
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220
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221 **Acknowledgments**
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222
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223 To convert the distance matrix to a Newick-formatted tree, we use the
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224 QuickTree program from
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225 http://www.sanger.ac.uk/resources/software/quicktree/ .
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226
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227 To make the diagram we use draw_tree, available at
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228 http://compgen.bscb.cornell.edu/phast/ .
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229
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230 </help>
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231 </tool>