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1 <tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@WRAPPER_VERSION@.3.0">
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2 <description>aligns integrated orthologous gene family clusters</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="requirements_gene_family_aligner" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 #set alignment_method = $alignment_method_cond.alignment_method
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9 #set input_dir = 'input_dir'
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10 mkdir $input_dir &&
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11 #for $i in $input:
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12 #set filename = $i.file_name
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13 #set name = $i.name
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14 ln -s $filename $input_dir/$name &&
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15 #end for
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16 GeneFamilyAligner
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17 --alignment_method $alignment_method
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18 #if str($alignment_method) == 'pasta':
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19 --pasta_script_path '$__tool_directory__/run_pasta.py'
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20 --pasta_iter_limit $alignment_method_cond.pasta_iter_limit
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21 #end if
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22 --num_threads \${GALAXY_SLOTS:-4}
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23 --orthogroup_faa '$input_dir'
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24 #if str($codon_alignments) == 'yes':
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25 --codon_alignments
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26 #end if
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27 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
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28 #if str($remove_gappy_sequences) == 'yes':
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29 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
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30 #set trim_type = $trim_type_cond.trim_type
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31 #if str($trim_type) == 'gap_trimming' and str($trim_type_cond.gap_trimming):
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32 --gap_trimming $trim_type_cond.gap_trimming
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33 #else:
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34 ## str($trim_type) == 'automated_trimming'
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35 --automated_trimming
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36
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36 #end if
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37 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond
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38 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps
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39 #if str($remove_sequences_with_gaps) == 'yes':
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40 #if str($remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of):
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41 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
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42 #end if
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43 #if str($remove_sequences_with_gaps_cond.iterative_realignment):
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44 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
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45 #end if
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46 #end if
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38
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47 #end if
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48 ]]></command>
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49 <inputs>
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50 <param name="input" format="fasta" type="data_collection" collection_type="list" label="Proteins orthogroup fasta files" />
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51 <expand macro="cond_alignment_method" />
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52 <expand macro="param_codon_alignments" />
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53 <expand macro="cond_remove_gappy_sequences" />
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54 </inputs>
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55 <outputs>
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56 <collection name="primary_faa" type="list" label="${tool.name} (primary orthogroup protein alignments) on ${on_string}">
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57 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln_faa" format="fasta" />
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58 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
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59 </collection>
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60 <collection name="trimmed_faa" type="list" label="${tool.name} (trimmed orthogroup protein alignments) on ${on_string}">
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61 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_trimmed_aln_faa" format="fasta" />
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62 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
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63 </collection>
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64 <collection name="filtered_faa" type="list" label="${tool.name} (filtered orthogroup protein alignments) on ${on_string}">
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65 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_faa" format="fasta" />
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66 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
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67 </collection>
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68 <collection name="pristine_faa" type="list" label="${tool.name} (primary orthogroup protein alignments) on ${on_string}">
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69 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" />
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70 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['output_pristine_alignments'] == 'yes'</filter>
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71 </collection>
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72 <collection name="primary_fna" type="list" label="${tool.name} (primary orthogroup codon alignments) on ${on_string}">
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73 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln_fna" format="fasta" />
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74 <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
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75 </collection>
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76 <collection name="trimmed_fna" type="list" label="${tool.name} (trimmed orthogroup codon alignments) on ${on_string}">
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77 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_trimmed_aln_fna" format="fasta" />
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78 <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
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79 </collection>
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80 <collection name="filtered_fna" type="list" label="${tool.name} (filtered orthogroup codon alignments) on ${on_string}">
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81 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_fna" format="fasta" />
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82 <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
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83 </collection>
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84 <collection name="pristine_fna" type="list" label="${tool.name} (primary orthogroup protein and codon alignments) on ${on_string}">
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85 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" />
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86 <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['output_pristine_alignments'] == 'yes'</filter>
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87 </collection>
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88 </outputs>
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89 <tests>
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90 <test>
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91 </test>
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92 </tests>
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93 <help>
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94 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary
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95 analyses of genome-scale gene families and transcriptomes. This tool estimates protein and codon multiple sequence alignments
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96 of integrated orthologous gene family fasta files produced by the GeneFamilyIntegrator tool.
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97
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98 -----
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99
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100 **Required options**
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101
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102 * **Classified orthogroup fasta files** - orthogroup fasta files produced by the GeneFamilyClassifier tool selected from your history. Depending on how the GeneFamilyClassifier tool was executed, these could either be proteins or proteins and their corresponding coding sequences.
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103
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104 * **Multiple sequence alignment method** - method for estimating orthogroup multiple sequence alignments. PlantTribes estimates alignments using either MAFFT's L-INS-i algorithm or the divide and conquer approach implemented in the PASTA pipeline for large alignments.
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105
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106 - **PASTA iteration limit** - number of PASTA iterations. By default, PASTA performs 3 iterations.
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107
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108 * **Codon alignments** - select 'Yes' to create codon multiple sequence alignments. This option requires protein and their corresponding coding sequences to be provided as input data.
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109
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110 **Other options**
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111
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112 * **Alignment post-processing configuration** - select 'Yes' to enable multiple sequence alignment post-processing configuration options.
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113
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114 - **Trimming method** - multiple sequence alignment trimming method. PlantTribes trims alignments using two automated approaches implemented in trimAl. Gap score based trimming removes alignments sites that do not achieve a user specified gap score. For example, a setting of 0.1 removes sites that have gaps in 90% or more of the sequences in the multiple sequence alignment. The automated heuristic trimming approach determines the best automated trimAl method to trim a given alignment as described in the trimAl tutorial `trimAl`_.
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115
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116 - **Gap score** - the fraction of sequences with gap allowed in an alignment site. The score is restricted to the range 0.0 - 1.0. Zero value has no effect.
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117
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118 - **Remove sequences** - select 'Yes' to remove sequences in multiple sequence alignments that do not achieve a user specified alignment coverage score. For example, a setting of 0.7 removes sequences with more than 30% gaps in the alignment. This option requires one of the trimming methods to be set.
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119
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120 - **Coverage score** - minimum fraction of sites without gaps for a sequence in a multiple sequence alignment. The score is restricted to the range 0.0 - 1.0. Zero value has no effect.
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121
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122 - **Realignment iteration limit** - number of iterations to perform trimming, removal of sequences, and realignment of orthogroup sequences. Zero value has no effect.
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123
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124 * **Output additional dataset collection of files** - selecting 'Yes' will produce an additional output dataset collection whose elements are copies of the directories of files (these elements can be viewed with visualization tools).
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125
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126 .. _trimAl: http://trimal.cgenomics.org
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127
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128 </help>
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129 <citations>
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130 <expand macro="citation1" />
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131 <citation type="bibtex">
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132 @article{Wall2008,
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133 journal = {Nucleic Acids Research},
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134 author = {2. Wall PK, Leebens-Mack J, Muller KF, Field D, Altman NS},
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135 title = {PlantTribes: a gene and gene family resource for comparative genomics in plants},
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136 year = {2008},
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137 volume = {36},
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138 number = {suppl 1},
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139 pages = {D970-D976},}
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140 </citation>
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141 <citation type="bibtex">
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142 @article{Katoh2013,
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143 journal = {Molecular biology and evolution},
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144 author = {3. Katoh K, Standley DM},
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145 title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
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146 year = {2013},
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147 volume = {30},
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148 number = {4},
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149 pages = {772-780},}
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150 </citation>
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151 <citation type="bibtex">
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152 @article{Mirarab2014,
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153 journal = {Research in Computational Molecular Biology (RECOMB)},
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154 author = {4. Mirarab S, Nguyen N, Warnow T},
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155 title = {PASTA: Ultra-Large Multiple Sequence Alignment. In R. Sharan (Ed.)},
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156 year = {2014},
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157 pages = {177–191},
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158 url = {https://github.com/smirarab/pasta},}
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159 </citation>
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160 <citation type="bibtex">
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161 @article{Capella-Gutierrez2009,
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162 journal = {Bioinformatics,},
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163 author = {5. Capella-Gutierrez S, Silla-Martínez JM, Gabaldón T},
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164 title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses},
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165 year = {2009},
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166 volume = {25},
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167 number = {15},
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168 pages = {1972-1973},}
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169 </citation>
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170 <citation type="bibtex">
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171 @article{Yachdav2016,
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172 journal = {Bioinformatics,},
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173 author = {6. Yachdav G, Wilzbach S, Rauscher B, Sheridan R, Sillitoe I, Procter J, Lewis SE, Rost B, Goldberg T},
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174 title = {MSAViewer: interactive JavaScript visualization of multiple sequence alignments},
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175 year = {2016},
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176 volume = {32},
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177 number = {22},
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178 pages = {3501-3503},}
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179 </citation>
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180 <citation type="bibtex">
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181 @article{Clamp2004,
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182 journal = {Bioinformatics,},
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183 author = {7. Clamp M, Cuff J, Searle SM, Barton GJ},
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184 title = {The jalview java alignment editor},
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185 year = {2004},
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186 volume = {20},
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187 number = {3},
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188 pages = {426-427},}
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189 </citation>
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190 </citations>
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191 </tool>
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