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1 <tool id="plant_tribes_assembly_post_processor" name="Postprocess de novo assembly transcripts" version="0.4.0">
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2 <description>into putative coding sequences</description>
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3 <requirements>
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4 <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement>
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5 </requirements>
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6 <stdio>
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7 <!-- Anything other than zero is an error -->
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8 <exit_code range="1:" />
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9 <exit_code range=":-1" />
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10 <!-- In case the return code has not been set propery check stderr too -->
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11 <regex match="Error:" />
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12 <regex match="Exception:" />
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13 </stdio>
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14 <command>
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15 <![CDATA[
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15
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16 #import os
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17 AssemblyPostProcesser
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18 --transcripts '$input'
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19 --prediction_method $prediction_method_cond.prediction_method
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20 #if str($prediction_method_cond.prediction_method) == 'estscan':
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21 --score_matrices '$score_matrices'
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22 #end if
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23 #if str($options_type.options_type_selector) == 'advanced':
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24 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
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25 --config_dir '$options_type.target_gene_family_assembly_cond.scaffold.fields.path'
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26 --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups'
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27 --scaffold '$options_type.target_gene_family_assembly_cond.scaffold.fields.path'
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28 --method '$options_type.target_gene_family_assembly_cond.method'
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29 #end if
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30 --gap_trimming $options_type.gap_trimming
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31 #if str($options_type.strand_specific) == 'yes':
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32 --strand_specific
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33 #end if
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34 #if str($options_type.dereplicate) == 'yes':
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35 --dereplicate
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36 #end if
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37 --min_length $options_type.min_length
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38 #end if
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39 --num_threads \${GALAXY_SLOTS:-4}
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40 ]]>
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41 </command>
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42 <inputs>
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43 <param name="input" format="fasta" type="data" label="De novo transcriptome assembly fasta file"/>
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44 <conditional name="prediction_method_cond">
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45 <param name="prediction_method" type="select" label="Prediction method for coding regions">
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46 <option value="transdecoder" selected="true">TransDecoder</option>
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47 <option value="estscan">ESTScan</option>
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48 </param>
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49 <when value="transdecoder" />
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50 <when value="estscan">
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51 <param name="score_matrices" format="smat" type="data" label="Scores matrices"/>
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52 </when>
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53 </conditional>
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54 <conditional name="options_type">
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55 <param name="options_type_selector" type="select" label="Options Configuration">
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56 <option value="basic" selected="true">Basic</option>
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57 <option value="advanced">Advanced</option>
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58 </param>
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59 <when value="basic" />
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60 <when value="advanced">
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61 <conditional name="target_gene_family_assembly_cond">
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62 <param name="target_gene_family_assembly" type="select" label="Target gene family assembly?">
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63 <option value="no" selected="true">No</option>
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64 <option value="yes">Yes</option>
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65 </param>
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66 <when value="no" />
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67 <when value="yes">
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68 <param name="orthogroups" format="tabular" type="data" label="List of orthogroup identifiers for target gene families to assemble"/>
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69 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
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70 <options from_data_table="plant_tribes_scaffolds" />
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71 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table."/>
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72 </param>
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73 <param name="method" type="select" label="Protein clustering method">
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74 <option value="gfam" selected="true">GFam</option>
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75 <option value="orthofinder">OrthoFinder</option>
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76 <option value="orthomcl">OrthoMCL</option>
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77 </param>
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78 </when>
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79 </conditional>
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80 <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="0.1 removes sites with 90% gaps"/>
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81 <param name="strand_specific" type="select" label="De novo transcriptome assembly was performed with strand-specific library?">
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82 <option value="no" selected="true">No</option>
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83 <option value="yes">Yes</option>
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84 </param>
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85 <param name="dereplicate" type="select" label="Remove repeated sequences in predicted coding regions?">
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86 <option value="no" selected="true">No</option>
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87 <option value="yes">Yes</option>
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88 </param>
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89 <param name="min_length" type="integer" value="200" label="Minimum sequence length of predicted coding regions"/>
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90 </when>
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91 </conditional>
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92 </inputs>
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93 <outputs>
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94 <collection name="transcripts" type="list">
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95 <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir" visible="true" ext="fasta" />
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96 </collection>
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97 </outputs>
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98 <tests>
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99 <test>
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100 <param name="input" value="assembly.fasta" ftype="fasta" />
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101 <param name="prediction_method" value="transdecoder" />
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102 <output_collection name="transcripts" type="list">
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103 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/>
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104 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/>
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105 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta"/>
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106 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
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107 </output_collection>
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108 </test>
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109 <test>
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110 <param name="input" value="assembly.fasta" ftype="fasta" />
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111 <param name="prediction_method" value="transdecoder" />
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112 <param name="options_type_selector" value="advanced" />
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113 <param name="gap_trimming" value="0.1" />
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114 <param name="dereplicate" value="yes" />
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115 <param name="min_length" value="200" />
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116 <output_collection name="transcripts" type="list">
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117 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/>
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118 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/>
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119 <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/>
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120 <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/>
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121 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta"/>
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122 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
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123 </output_collection>
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124 </test>
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125 </tests>
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126 <help>
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127 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
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128 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It postprocesses de novo assembly
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129 transcripts into putative coding sequences and their corresponding amino acid translations, locally assembling targeted gene families.
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130
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131 -----
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132
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133 **Options**
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134
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135 * **Prediction method for coding regions** - The prediction method for coding regions; one of ESTScan or TransDecoder.
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136 * **Scores matrices** - Scores matrices that reflect the codons preferences in the studied organisms.
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137 * **Target gene family assembly?** - Select 'Yes' to target gene families to assemble.
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138 * **List of orthogroup identifiers for target gene families to assemble** - History item with a list of orthogroup identifiers for target gene families to assemble.
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139 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data installed into Galaxy by the PlantTribes Scaffolds Download Data Manager tool.
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140 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
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141 * **Remove sites in alignments with gaps of** - Removes gappy sites in alignments (i.e. 0.1 removes sites with 90% gaps): [0.0 to 1.0]
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142 * **De novo transcriptome assembly was performed with strand-specific library?** - Select 'Yes' if de novo transcriptome assembly was performed with strand-specific library.
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143 * **Remove repeated sequences in predicted coding regions?** - Select yes to remove repeated sequences in predicted coding regions.
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144 * **Minimum sequence length of predicted coding regions** - Set the minimum sequence length of predicted coding regions.
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145
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146 </help>
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147 <citations>
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148 <citation type="bibtex">
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149 @unpublished{None,
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150 author = {Eric Wafula},
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151 title = {None},
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152 year = {None},
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153 url = {https://github.com/dePamphilis/PlantTribes}
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154 }</citation>
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155 <citation type="bibtex">
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156 @published{Proc Int Conf Intell Syst Mol Biol,
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157 author = {Iseli C, Jongeneel CV, Bucher P.},
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158 title = {ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences.},
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159 year = {1999},
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160 url = {http://estscan.sourceforge.net/}
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161 }</citation>
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162 <citation type="doi">10.1038/nprot.2013.084</citation>
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163 <citation type="doi">10.1109/tcbb.2013.68</citation>
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164 <citation type="bibtex">
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165 @unpublished{None,
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166 author = {None},
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167 title = {HMMER 3.1+ hmmscan search sequence(s) against a profile database},
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168 year = {2013},
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169 url = {http://hmmer.org/}
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170 }</citation>
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171 <citation type="bibtex">
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172 @published{Genome Research,
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173 author = {Huang X, Madan A},
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174 title = {CAP3: A DNA sequence assembly program},
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175 year = {1999},
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176 url = {http://seq.cs.iastate.edu/cap3.html}
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177 }</citation>
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178 </citations>
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179 </tool>
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