Mercurial > repos > iuc > funannotate_annotate

annotate macros.xml @ 0:a5baa4ff168d draft

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"planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
author iuc
date Mon, 04 Oct 2021 19:39:38 +0000
parents
children 78407487f758
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1 <?xml version="1.0"?>
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2 <macros>
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3 <token name="@TOOL_VERSION@">1.8.9</token>
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4 <token name="@VERSION_SUFFIX@">1</token>
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5
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6 <xml name="requirements">
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7 <requirement type="package" version="@TOOL_VERSION@">funannotate</requirement>
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8 </xml>
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9
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10 <xml name="citations">
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11 <citations>
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12 <citation type="doi">10.5281/zenodo.4054262</citation>
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13 </citations>
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14 </xml>
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15
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16 <xml name="augustus_species">
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17 <!-- list generated from a Funannotate database directory, listing trained_species/* -->
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18 <option value="adorsata">adorsata</option>
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19 <option value="aedes">aedes</option>
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20 <option value="amphimedon">amphimedon</option>
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21 <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
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22 <option value="anidulans">anidulans</option>
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23 <option value="arabidopsis">arabidopsis</option>
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24 <option value="aspergillus_fumigatus">aspergillus_fumigatus</option>
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25 <option value="aspergillus_nidulans">aspergillus_nidulans</option>
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26 <option value="aspergillus_oryzae">aspergillus_oryzae</option>
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27 <option value="aspergillus_terreus">aspergillus_terreus</option>
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28 <option value="bombus_impatiens1">bombus_impatiens1</option>
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29 <option value="bombus_terrestris2">bombus_terrestris2</option>
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30 <option value="botrytis_cinerea">botrytis_cinerea</option>
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31 <option value="b_pseudomallei">b_pseudomallei</option>
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32 <option value="brugia">brugia</option>
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33 <option value="cacao">cacao</option>
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34 <option value="caenorhabditis">caenorhabditis</option>
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35 <option value="camponotus_floridanus">camponotus_floridanus</option>
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36 <option value="candida_albicans">candida_albicans</option>
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37 <option value="candida_guilliermondii">candida_guilliermondii</option>
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38 <option value="candida_tropicalis">candida_tropicalis</option>
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39 <option value="c_elegans_trsk">c_elegans_trsk</option>
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40 <option value="chaetomium_globosum">chaetomium_globosum</option>
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41 <option value="chicken">chicken</option>
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42 <option value="chiloscyllium">chiloscyllium</option>
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43 <option value="chlamy2011">chlamy2011</option>
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44 <option value="chlamydomonas">chlamydomonas</option>
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45 <option value="chlorella">chlorella</option>
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46 <option value="ciona">ciona</option>
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47 <option value="coccidioides_immitis">coccidioides_immitis</option>
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48 <option value="Conidiobolus_coronatus">Conidiobolus_coronatus</option>
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49 <option value="coprinus">coprinus</option>
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50 <option value="coprinus_cinereus">coprinus_cinereus</option>
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51 <option value="coyote_tobacco">coyote_tobacco</option>
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52 <option value="cryptococcus">cryptococcus</option>
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53 <option value="cryptococcus_neoformans_gattii">cryptococcus_neoformans_gattii</option>
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54 <option value="cryptococcus_neoformans_neoformans_B">cryptococcus_neoformans_neoformans_B</option>
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55 <option value="cryptococcus_neoformans_neoformans_JEC21">cryptococcus_neoformans_neoformans_JEC21</option>
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56 <option value="culex">culex</option>
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57 <option value="debaryomyces_hansenii">debaryomyces_hansenii</option>
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58 <option value="E_coli_K12">E_coli_K12</option>
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59 <option value="elephant_shark">elephant_shark</option>
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60 <option value="encephalitozoon_cuniculi_GB">encephalitozoon_cuniculi_GB</option>
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61 <option value="eremothecium_gossypii">eremothecium_gossypii</option>
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62 <option value="fly">fly</option>
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63 <option value="fly_exp">fly_exp</option>
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64 <option value="fusarium">fusarium</option>
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65 <option value="fusarium_graminearum">fusarium_graminearum</option>
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66 <option value="galdieria">galdieria</option>
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67 <option value="generic">generic</option>
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68 <option value="heliconius_melpomene1">heliconius_melpomene1</option>
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69 <option value="histoplasma">histoplasma</option>
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70 <option value="histoplasma_capsulatum">histoplasma_capsulatum</option>
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71 <option value="honeybee1">honeybee1</option>
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72 <option value="human">human</option>
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73 <option value="japaneselamprey">japaneselamprey</option>
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74 <option value="kluyveromyces_lactis">kluyveromyces_lactis</option>
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75 <option value="laccaria_bicolor">laccaria_bicolor</option>
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76 <option value="leishmania_tarentolae">leishmania_tarentolae</option>
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77 <option value="lodderomyces_elongisporus">lodderomyces_elongisporus</option>
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78 <option value="magnaporthe_grisea">magnaporthe_grisea</option>
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79 <option value="maize">maize</option>
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80 <option value="maize5">maize5</option>
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81 <option value="mnemiopsis_leidyi">mnemiopsis_leidyi</option>
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82 <option value="nasonia">nasonia</option>
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83 <option value="nematostella_vectensis">nematostella_vectensis</option>
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84 <option value="neurospora">neurospora</option>
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85 <option value="neurospora_crassa">neurospora_crassa</option>
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86 <option value="parasteatoda">parasteatoda</option>
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87 <option value="pchrysosporium">pchrysosporium</option>
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88 <option value="pea_aphid">pea_aphid</option>
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89 <option value="pfalciparum">pfalciparum</option>
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90 <option value="phanerochaete_chrysosporium">phanerochaete_chrysosporium</option>
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91 <option value="pichia_stipitis">pichia_stipitis</option>
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92 <option value="pisaster">pisaster</option>
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93 <option value="pneumocystis">pneumocystis</option>
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94 <option value="rhincodon">rhincodon</option>
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95 <option value="rhizopus_oryzae">rhizopus_oryzae</option>
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96 <option value="rhodnius">rhodnius</option>
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97 <option value="rice">rice</option>
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98 <option value="saccharomyces">saccharomyces</option>
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99 <option value="saccharomyces_cerevisiae_rm11-1a_1">saccharomyces_cerevisiae_rm11-1a_1</option>
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100 <option value="saccharomyces_cerevisiae_S288C">saccharomyces_cerevisiae_S288C</option>
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101 <option value="s_aureus">s_aureus</option>
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102 <option value="schistosoma">schistosoma</option>
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103 <option value="schistosoma2">schistosoma2</option>
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iuc
parents:
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104 <option value="schizosaccharomyces_pombe">schizosaccharomyces_pombe</option>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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105 <option value="scyliorhinus">scyliorhinus</option>
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iuc
parents:
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106 <option value="sealamprey">sealamprey</option>
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iuc
parents:
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107 <option value="s_pneumoniae">s_pneumoniae</option>
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iuc
parents:
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108 <option value="strongylocentrotus_purpuratus">strongylocentrotus_purpuratus</option>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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109 <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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110 <option value="template_prokaryotic">template_prokaryotic</option>
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iuc
parents:
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111 <option value="tetrahymena">tetrahymena</option>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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112 <option value="thermoanaerobacter_tengcongensis">thermoanaerobacter_tengcongensis</option>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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113 <option value="tomato">tomato</option>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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114 <option value="toxoplasma">toxoplasma</option>
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iuc
parents:
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115 <option value="tribolium2012">tribolium2012</option>
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iuc
parents:
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116 <option value="trichinella">trichinella</option>
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iuc
parents:
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117 <option value="ustilago">ustilago</option>
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iuc
parents:
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118 <option value="ustilago_maydis">ustilago_maydis</option>
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iuc
parents:
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119 <option value="verticillium_albo_atrum1">verticillium_albo_atrum1</option>
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iuc
parents:
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120 <option value="verticillium_longisporum1">verticillium_longisporum1</option>
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iuc
parents:
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121 <option value="volvox">volvox</option>
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iuc
parents:
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122 <option value="wheat">wheat</option>
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iuc
parents:
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123 <option value="Xipophorus_maculatus">Xipophorus_maculatus</option>
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iuc
parents:
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124 <option value="yarrowia_lipolytica">yarrowia_lipolytica</option>
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iuc
parents:
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125 <option value="zebrafish">zebrafish</option>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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126 </xml>
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iuc
parents:
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127
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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128 <xml name="busco_species">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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129 <!-- list generated from a Funannotate database directory, with the "funannotate database -show-buscos command" -->
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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130 <option value="eukaryota">eukaryota</option>
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iuc
parents:
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131 <option value="metazoa">metazoa</option>
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parents:
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132 <option value="nematoda">nematoda</option>
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iuc
parents:
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133 <option value="arthropoda">arthropoda</option>
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iuc
parents:
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134 <option value="insecta">insecta</option>
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iuc
parents:
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135 <option value="endopterygota">endopterygota</option>
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iuc
parents:
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136 <option value="hymenoptera">hymenoptera</option>
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iuc
parents:
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137 <option value="diptera">diptera</option>
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iuc
parents:
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138 <option value="vertebrata">vertebrata</option>
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iuc
parents:
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139 <option value="actinopterygii">actinopterygii</option>
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iuc
parents:
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140 <option value="tetrapoda">tetrapoda</option>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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141 <option value="aves">aves</option>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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142 <option value="mammalia">mammalia</option>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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143 <option value="euarchontoglires">euarchontoglires</option>
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iuc
parents:
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144 <option value="laurasiatheria">laurasiatheria</option>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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145 <option value="fungi">fungi</option>
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iuc
parents:
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146 <option value="dikarya">dikarya</option>
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iuc
parents:
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147 <option value="ascomycota">ascomycota</option>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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148 <option value="pezizomycotina">pezizomycotina</option>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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149 <option value="eurotiomycetes">eurotiomycetes</option>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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150 <option value="sordariomycetes">sordariomycetes</option>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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151 <option value="saccharomycetes">saccharomycetes</option>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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152 <option value="saccharomycetales">saccharomycetales</option>
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iuc
parents:
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153 <option value="basidiomycota">basidiomycota</option>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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154 <option value="microsporidia">microsporidia</option>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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155 <option value="embryophyta">embryophyta</option>
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iuc
parents:
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156 <option value="protists">protists</option>
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iuc
parents:
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157 <option value="alveolata_stramenophiles">alveolata_stramenophiles</option>
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iuc
parents:
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158 </xml>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
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159 </macros>