Mercurial > repos > jjohnson > mothur_toolsuite

annotate mothur/suite_config.xml @ 2:e076d95dbdb5

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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author jjohnson
date Tue, 07 Jun 2011 17:05:08 -0400
parents c7923b34dea4
children
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2
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1 <suite id="Mothur_toolsuite" name="Mothur Metagenomics" version="1.19.0">
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2 <description>Mothur metagenomics commands as Galaxy tools</description>
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3 <tool id="mothur_align_check" name="Align.check" version="1.19.0">
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4 <description>Calculate the number of potentially misaligned bases</description>
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5 </tool>
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6 <tool id="mothur_align_seqs" name="Align.seqs" version="1.19.0">
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7 <description>Align sequences to a template alignment</description>
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8 </tool>
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9 <tool id="mothur_amova" name="Amova" version="1.19.0">
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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10 <description>Analysis of molecular variance</description>
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11 </tool>
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12 <tool id="mothur_anosim" name="Anosim" version="1.19.0">
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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13 <description>Non-parametric multivariate analysis of changes in community structure</description>
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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14 </tool>
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15 <tool id="mothur_bin_seqs" name="Bin.seqs" version="1.19.0">
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16 <description>Order Sequences by OTU</description>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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17 </tool>
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e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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18 <tool id="mothur_chimera_bellerophon" name="Chimera.bellerophon" version="1.19.0">
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19 <description>Find putative chimeras using bellerophon</description>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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20 </tool>
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21 <tool id="mothur_chimera_ccode" name="Chimera.ccode" version="1.19.0">
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22 <description>Find putative chimeras using ccode</description>
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23 </tool>
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24 <tool id="mothur_chimera_check" name="Chimera.check" version="1.19.0">
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25 <description>Find putative chimeras using chimeraCheck</description>
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26 </tool>
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27 <tool id="mothur_chimera_pintail" name="Chimera.pintail" version="1.19.0">
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28 <description>Find putative chimeras using pintail</description>
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29 </tool>
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30 <tool id="mothur_chimera_slayer" name="Chimera.slayer" version="1.19.0">
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31 <description>Find putative chimeras using slayer</description>
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32 </tool>
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33 <tool id="mothur_chop_seqs" name="Chop.seqs" version="1.19.0">
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34 <description>Trim sequences to a specified length</description>
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35 </tool>
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36 <tool id="mothur_classify_otu" name="Classify.otu" version="1.19.0">
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37 <description>Assign sequences to taxonomy</description>
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38 </tool>
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39 <tool id="mothur_classify_seqs" name="Classify.seqs" version="1.19.0">
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40 <description>Assign sequences to taxonomy</description>
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41 </tool>
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42 <tool id="mothur_clearcut" name="Clearcut" version="1.19.0">
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43 <description>Generate a tree using relaxed neighbor joining</description>
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44 </tool>
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45 <tool id="mothur_cluster_classic" name="Cluster.classic" version="1.19.0">
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46 <description>Assign sequences to OTUs (Dotur implementation)</description>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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47 </tool>
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48 <tool id="mothur_cluster_fragments" name="Cluster.fragments" version="1.19.0">
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49 <description> Group sequences that are part of a larger sequence</description>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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50 </tool>
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51 <tool id="mothur_cluster_split" name="Cluster.split" version="1.19.0">
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52 <description>Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices</description>
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53 </tool>
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54 <tool id="mothur_cluster" name="Cluster" version="1.19.0">
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55 <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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56 </tool>
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57 <tool id="mothur_collect_shared" name="Collect.shared" version="1.19.0">
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58 <description>Generate collector's curves for calculators on OTUs</description>
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59 </tool>
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60 <tool id="mothur_collect_single" name="Collect.single" version="1.19.0">
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61 <description>Generate collector's curves for OTUs</description>
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62 </tool>
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63 <tool id="mothur_consensus_seqs" name="Consensus.seqs" version="1.19.0">
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64 <description>Find a consensus sequence for each OTU or phylotype</description>
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65 </tool>
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66 <tool id="mothur_corr_axes" name="Corr.axes" version="1.19.0">
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67 <description>correlation of data to axes</description>
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68 </tool>
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69 <tool id="mothur_degap_seqs" name="Degap.seqs" version="1.19.0">
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70 <description>Remove gap characters from sequences</description>
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71 </tool>
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72 <tool id="mothur_deunique_seqs" name="Deunique.seqs" version="1.19.0">
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73 <description>Return all sequences</description>
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74 </tool>
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75 <tool id="mothur_dist_seqs" name="Dist.seqs" version="1.19.0">
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76 <description>calculate uncorrected pairwise distances between aligned sequences</description>
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77 </tool>
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78 <tool id="mothur_dist_shared" name="Dist.shared" version="1.19.0">
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79 <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</description>
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80 </tool>
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81 <tool id="mothur_fastq_info" name="Fastq.info" version="1.19.0">
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82 <description>Convert fastq to fasta and quality</description>
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83 </tool>
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84 <tool id="mothur_filter_seqs" name="Filter.seqs" version="1.19.0">
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85 <description>removes columns from alignments</description>
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86 </tool>
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87 <tool id="mothur_get_groups" name="Get.groups" version="1.19.0">
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88 <description>Select groups</description>
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89 </tool>
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90 <tool id="mothur_get_group" name="Get.group" version="1.19.0">
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91 <description>group names from shared or from list and group</description>
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92 </tool>
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93 <tool id="mothur_get_lineage" name="Get.lineage" version="1.19.0">
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94 <description>Picks by taxon</description>
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95 </tool>
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96 <tool id="mothur_get_otulist" name="Get.otulist" version="1.19.0">
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97 <description>Get otus for each distance in a otu list</description>
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98 </tool>
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99 <tool id="mothur_get_oturep" name="Get.oturep" version="1.19.0">
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100 <description>Generate a fasta with a representative sequence for each OTU</description>
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101 </tool>
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102 <tool id="mothur_get_otus" name="Get.otus" version="1.19.0">
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103 <description>Get otus containing sequences from specified groups</description>
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104 </tool>
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105 <tool id="mothur_get_rabund" name="Get.rabund" version="1.19.0">
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106 <description>Get rabund from a otu list or sabund</description>
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107 </tool>
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108 <tool id="mothur_get_relabund" name="Get.relabund" version="1.19.0">
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109 <description>Calculate the relative abundance of each otu</description>
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110 </tool>
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111 <tool id="mothur_get_sabund" name="Get.sabund" version="1.19.0">
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112 <description>Get sabund from a otu list or rabund</description>
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113 </tool>
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114 <tool id="mothur_get_seqs" name="Get.seqs" version="1.19.0">
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115 <description>Picks sequences by name</description>
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116 </tool>
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117 <tool id="mothur_get_sharedseqs" name="Get.sharedseqs" version="1.19.0">
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118 <description>Get shared sequences at each distance from list and group</description>
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119 </tool>
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120 <tool id="mothur_hcluster" name="Hcluster" version="1.19.0">
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121 <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description>
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122 </tool>
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123 <tool id="mothur_heatmap_bin" name="Heatmap.bin" version="1.19.0">
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124 <description>Generate a heatmap for OTUs</description>
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125 </tool>
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126 <tool id="mothur_heatmap_sim" name="Heatmap.sim" version="1.19.0">
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127 <description>Generate a heatmap for pariwise similarity</description>
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128 </tool>
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129 <tool id="mothur_homova" name="Homova" version="1.19.0">
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130 <description>Homogeneity of molecular variance</description>
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diff changeset
131 </tool>
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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132 <tool id="mothur_indicator" name="Indicator" version="1.19.0">
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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133 <description>Identify indicator "species" for nodes on a tree</description>
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jjohnson
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134 </tool>
2
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135 <tool id="mothur_libshuff" name="Libshuff" version="1.19.0">
0
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136 <description>Cramer-von Mises tests communities for the same structure</description>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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137 </tool>
2
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jjohnson
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138 <tool id="mothur_list_seqs" name="List.seqs" version="1.19.0">
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
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139 <description>Lists the names (accnos) of the sequences</description>
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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140 </tool>
2
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jjohnson
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141 <tool id="mothur_make_design" name="Make Design" version="1.19.0" >
1
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
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142 <description>Assign groups to Sets</description>
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jjohnson
parents: 0
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143 </tool>
2
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jjohnson
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144 <tool id="mothur_make_fastq" name="Make.fastq" version="1.19.0">
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jjohnson
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145 <description>Convert fasta and quality to fastq</description>
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
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146 </tool>
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
147 <tool id="mothur_make_files" name="Make.group" version="1.19.0">
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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148 <description>Make a group file</description>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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149 </tool>
2
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150 <tool id="mothur_make_shared" name="Make.shared" version="1.19.0">
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jjohnson
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151 <description>Make a shared file from a list and a group</description>
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jjohnson
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152 </tool>
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153 <tool id="mothur_mantel" name="Mantel" version="1.19.0">
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
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154 <description>Mantel correlation coefficient between two matrices.</description>
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
155 </tool>
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
156 <tool id="mothur_merge_files" name="Merge.files" version="1.19.0">
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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157 <description>Merge data</description>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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158 </tool>
2
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jjohnson
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159 <tool id="mothur_merge_groups" name="Merge.groups" version="1.19.0" >
1
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
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160 <description>Merge groups in a shared file</description>
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
161 </tool>
2
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jjohnson
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162 <tool id="mothur_metastats" name="Metastats" version="1.19.0" >
1
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
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163 <description>generate principle components plot data</description>
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
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164 </tool>
2
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jjohnson
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165 <tool id="mothur_nmds" name="Nmds" version="1.19.0">
1
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
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166 <description>generate non-metric multidimensional scaling data</description>
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
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167 </tool>
2
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jjohnson
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168 <tool id="mothur_normalize_shared" name="Normalize.shared" version="1.19.0">
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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169 <description>Normalize the number of sequences per group to a specified level</description>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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170 </tool>
2
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171 <tool id="mothur_otu_hierarchy" name="Otu.hierarchy" version="1.19.0">
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172 <description>Relate OTUs at different distances</description>
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173 </tool>
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174 <tool id="mothur_pairwise_seqs" name="Pairwise.seqs" version="1.19.0">
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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175 <description>calculate uncorrected pairwise distances between sequences</description>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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176 </tool>
2
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177 <tool id="mothur_parse_list" name="Parse.list" version="1.19.0">
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178 <description>Generate a List file for each group</description>
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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179 </tool>
2
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180 <tool id="mothur_parsimony" name="Parsimony" version="1.19.0">
0
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181 <description>Describes whether two or more communities have the same structure</description>
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jjohnson
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182 </tool>
2
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183 <tool id="mothur_pca" name="Pca" version="1.19.0">
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jjohnson
parents: 1
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184 <description>Principal Coordinate Analysis for a shared file</description>
1
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jjohnson
parents: 0
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185 </tool>
2
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186 <tool id="mothur_pcoa" name="Pcoa" version="1.19.0" >
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
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187 <description>Principal Coordinate Analysis for a distance matrix</description>
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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188 </tool>
2
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189 <tool id="mothur_phylo_diversity" name="Phylo.diversity" version="1.19.0">
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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190 <description>Alpha Diversity calculates unique branch length</description>
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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191 </tool>
2
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192 <tool id="mothur_phylotype" name="Phylotype" version="1.19.0">
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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193 <description>Assign sequences to OTUs based on taxonomy</description>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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194 </tool>
2
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195 <tool id="mothur_pre_cluster" name="Pre.cluster" version="1.19.0">
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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196 <description>Remove sequences due to pyrosequencing errors</description>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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197 </tool>
2
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198 <tool id="mothur_rarefaction_shared" name="Rarefaction.shared" version="1.19.0">
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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199 <description>Generate inter-sample rarefaction curves for OTUs</description>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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200 </tool>
2
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201 <tool id="mothur_rarefaction_single" name="Rarefaction.single" version="1.19.0">
0
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jjohnson
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202 <description>Generate intra-sample rarefaction curves for OTUs</description>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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203 </tool>
2
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204 <tool id="mothur_remove_groups" name="Remove.groups" version="1.19.0">
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
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205 <description>Remove groups from groups,fasta,names,list,taxonomy</description>
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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206 </tool>
2
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207 <tool id="mothur_remove_lineage" name="Remove.lineage" version="1.19.0">
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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208 <description>Picks by taxon</description>
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209 </tool>
2
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210 <tool id="mothur_remove_otus" name="Remove.otus" version="1.19.0">
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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211 <description>Remove otus containing sequences from specified groups</description>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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212 </tool>
2
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jjohnson
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213 <tool id="mothur_remove_rare" name="Remove.rare" version="1.19.0">
1
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
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214 <description>Remove rare OTUs</description>
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
215 </tool>
2
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jjohnson
parents: 1
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216 <tool id="mothur_remove_seqs" name="Remove.seqs" version="1.19.0">
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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217 <description>Remove sequences by name</description>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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218 </tool>
2
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219 <tool id="mothur_reverse_seqs" name="Reverse.seqs" version="1.19.0">
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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220 <description>Reverse complement the sequences</description>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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221 </tool>
2
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222 <tool id="mothur_screen_seqs" name="Screen.seqs" version="1.19.0">
0
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223 <description>Screen sequences</description>
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jjohnson
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224 </tool>
2
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225 <tool id="mothur_sens_spec" name="Sens.spec" version="1.19.0" >
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jjohnson
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226 <description>Determine the quality of OTU assignment</description>
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227 </tool>
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228 <tool id="mothur_sffinfo" name="Sffinfo" version="1.19.0">
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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229 <description>Summarize the quality of sequences</description>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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230 </tool>
2
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231 <tool id="mothur_split_abund" name="Split.abund" version="1.19.0">
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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232 <description>Separate sequences into rare and abundant groups</description>
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jjohnson
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233 </tool>
2
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234 <tool id="mothur_split_groups" name="Split.groups" version="1.19.0">
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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235 <description>Generates a fasta file for each group</description>
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jjohnson
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236 </tool>
2
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237 <tool id="mothur_sub_sample" name="Sub.sample" version="1.19.0">
0
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jjohnson
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238 <description>Create a sub sample</description>
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jjohnson
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239 </tool>
2
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240 <tool id="mothur_summary_seqs" name="Summary.seqs" version="1.19.0">
0
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jjohnson
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241 <description>Summarize the quality of sequences</description>
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jjohnson
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242 </tool>
2
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243 <tool id="mothur_summary_shared" name="Summary.shared" version="1.19.0">
0
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244 <description>Summary of calculator values for OTUs</description>
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245 </tool>
2
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246 <tool id="mothur_summary_single" name="Summary.single" version="1.19.0">
1
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jjohnson
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247 <description>Summary of calculator values for OTUs</description>
0
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248 </tool>
2
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249 <tool id="mothur_tree_shared" name="Tree.shared" version="1.19.0">
1
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jjohnson
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250 <description>Generate a newick tree for dissimilarity among groups</description>
0
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251 </tool>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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252 <tool id="tree_vector" name="TreeVector" version="1.0">
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253 <description>Draw a Phylogenic Tree</description>
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254 </tool>
2
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255 <tool id="mothur_trim_seqs" name="Trim.seqs" version="1.19.0">
1
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jjohnson
parents: 0
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256 <description>Trim sequences - primers, barcodes, quality</description>
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jjohnson
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257 </tool>
2
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258 <tool id="mothur_unifrac_unweighted" name="unifrac.unweighted" version="1.19.0">
1
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jjohnson
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259 <description>Describes whether two or more communities have the same structure</description>
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260 </tool>
2
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261 <tool id="mothur_unifrac_weighted" name="unifrac.weighted" version="1.19.0">
1
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262 <description>Describes whether two or more communities have the same structure</description>
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263 </tool>
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264 <tool id="mothur_unique_seqs" name="Unique.seqs" version="1.19.0">
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265 <description>Return unique sequences</description>
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266 </tool>
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267 <tool id="mothur_venn" name="Venn" version="1.19.0">
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268 <description>Generate Venn diagrams for groups </description>
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269 </tool>
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270 </suite>