Mercurial > repos > iuc > iqtree

annotate iqtree.xml @ 1:f041f5a855cc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
author iuc
date Sat, 25 Nov 2017 18:16:53 -0500
parents 72ef801e8d98
children b2fbfb61f019
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1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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1 <tool id="iqtree" name="IQ-TREE" version="1.5.5.1" >
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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2 <description>Phylogenomic / evolutionary tree construction from multiple sequences</description>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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3 <requirements>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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4 <requirement type="package" version="1.5.5">iqtree</requirement>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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5 </requirements>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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6 <command detect_errors='exit_code' ><![CDATA[
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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7 iqtree
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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8 -pre PREF
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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9 -nt \${GALAXY_SLOTS:-10}
0
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10 -redo
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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12 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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13 #if $general_options.s
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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14 -s '$general_options.s'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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15 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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17 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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18 #if $general_options.t
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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19 -t '$general_options.t'
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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20 $tree_parameters.constructing_consensus.con
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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21 $tree_parameters.constructing_consensus.net
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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22 #if str($tree_parameters.constructing_consensus.bi) != ''
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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23 -bi '$tree_parameters.constructing_consensus.bi'
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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24 #end if
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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26 ## file
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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27 #if $tree_parameters.constructing_consensus.sup
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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28 -sup '$tree_parameters.constructing_consensus.sup'
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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29 #end if
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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30
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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31 #if str($tree_parameters.constructing_consensus.suptag) != ''
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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32 -suptag '$tree_parameters.constructing_consensus.suptag'
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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33 #end if
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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35 ## file
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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36 #if $tree_parameters.computing_robinson_foulds.rf
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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37 -rf '$tree_parameters.computing_robinson_foulds.rf'
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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38 $tree_parameters.computing_robinson_foulds.rf_all
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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39 $tree_parameters.computing_robinson_foulds.rf_adj
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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40 #end if
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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41 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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43 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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44 #if $general_options.te
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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45 -te '$general_options.te'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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46 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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47
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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48 #if str($general_options.st) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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49 -st '$general_options.st'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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50 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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51
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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52 #if str($general_options.seed) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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53 -seed '$general_options.seed'
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54 #end if
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55
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56 $general_options.keep_ident
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57 $general_options.safe
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58
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59 #if str($likelihood_mapping.lmap) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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60 -lmap '$likelihood_mapping.lmap'
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61 #end if
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62
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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63 ## file
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64 #if $likelihood_mapping.lmclust
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65 -lmclust '$likelihood_mapping.lmclust'
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66 #end if
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67
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68 $likelihood_mapping.wql
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69
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70 #if str($modelling_parameters.automatic_model.cond_model.m) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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71 -m '$modelling_parameters.automatic_model.cond_model.m'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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72 #end if
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73
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74 #if str($modelling_parameters.automatic_model.rcluster) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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75 -rcluster '$modelling_parameters.automatic_model.rcluster'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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76 #end if
1
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77
0
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78 #if str($modelling_parameters.automatic_model.mset) != ''
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79 -mset '$modelling_parameters.automatic_model.mset'
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80 #end if
1
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81
0
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82 #if str($modelling_parameters.automatic_model.msub) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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83 -msub '$modelling_parameters.automatic_model.msub'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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84 #end if
1
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85
0
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86 #if str($modelling_parameters.automatic_model.mfreq) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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87 -mfreq '$modelling_parameters.automatic_model.mfreq'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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88 #end if
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89
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90 #if str($modelling_parameters.automatic_model.mrate) != ''
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91 -mrate '$modelling_parameters.automatic_model.mrate'
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92 #end if
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93
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
94 #if str($modelling_parameters.automatic_model.cmin) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
95 -cmin '$modelling_parameters.automatic_model.cmin'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
96 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
97
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
98 #if str($modelling_parameters.automatic_model.cmax) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
99 -cmax '$modelling_parameters.automatic_model.cmax'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
100 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
101
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
102 #if str($modelling_parameters.automatic_model.merit) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
103 -merit '$modelling_parameters.automatic_model.merit'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
104 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
105
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
106 $modelling_parameters.automatic_model.mtree
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
107
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
108 #if str($modelling_parameters.automatic_model.madd) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
109 -madd '$modelling_parameters.automatic_model.madd'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
110 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
111
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
112 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
113 #if $modelling_parameters.automatic_model.mdef
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
114 -mdef '$modelling_parameters.automatic_model.mdef'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
115 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
116
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
117 $modelling_parameters.specifying_substitution.mwopt
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
118
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
119 #if str($modelling_parameters.rate_heterogeneity.a) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
120 -a '$modelling_parameters.rate_heterogeneity.a'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
121 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
122
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
123 $modelling_parameters.rate_heterogeneity.gmedian
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
124
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
125 #if str($modelling_parameters.rate_heterogeneity.i) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
126 -i '$modelling_parameters.rate_heterogeneity.i'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
127 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
128
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
129 $modelling_parameters.rate_heterogeneity.opt_gamma_inv
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
130 $modelling_parameters.rate_heterogeneity.wsr
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
131
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
132 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
133 #if $modelling_parameters.partition_model.q
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
134 -q '$modelling_parameters.partition_model.q'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
135 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
136
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
137 $modelling_parameters.partition_model.spp
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
138
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
139 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
140 #if $modelling_parameters.partition_model.sp
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
141 -sp '$modelling_parameters.partition_model.sp'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
142 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
143
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
144 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
145 #if $modelling_parameters.site_specific_frequency.ft
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
146 -ft '$modelling_parameters.site_specific_frequency.ft'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
147 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
148
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
149 #if str($modelling_parameters.site_specific_frequency.fs) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
150 -fs '$modelling_parameters.site_specific_frequency.fs'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
151 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
152
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
153 $modelling_parameters.site_specific_frequency.fmax
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
154
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
155 #if str($tree_parameters.tree_search.ninit) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
156 -ninit '$tree_parameters.tree_search.ninit'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
157 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
158
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
159 #if str($tree_parameters.tree_search.ntop) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
160 -ntop '$tree_parameters.tree_search.ntop'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
161 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
162
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
163 #if str($tree_parameters.tree_search.nbest) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
164 -nbest '$tree_parameters.tree_search.nbest'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
165 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
166
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
167 #if str($tree_parameters.tree_search.nstop) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
168 -nstop '$tree_parameters.tree_search.nstop'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
169 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
170
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
171 #if str($tree_parameters.tree_search.n) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
172 -n '$tree_parameters.tree_search.n'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
173 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
174
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
175 #if str($tree_parameters.tree_search.sprrad) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
176 -sprrad '$tree_parameters.tree_search.sprrad'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
177 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
178
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
179 #if str($tree_parameters.tree_search.pers) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
180 -pers '$tree_parameters.tree_search.pers'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
181 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
182
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
183 $tree_parameters.tree_search.allnni
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
184 $tree_parameters.tree_search.djc
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
185
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
186 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
187 #if $tree_parameters.tree_search.g
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
188 -g '$tree_parameters.tree_search.g'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
189 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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190
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191 #if str($tree_parameters.single_branch.alrt) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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192 -alrt '$tree_parameters.single_branch.alrt'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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193 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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194
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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195 $tree_parameters.single_branch.abayes
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196
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iuc
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197 #if str($tree_parameters.single_branch.lbp) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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198 -lbp '$tree_parameters.single_branch.lbp'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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199 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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200
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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201 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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202 #if $tree_parameters.tree_topology.z
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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203 -z '$tree_parameters.tree_topology.z'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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204 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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205
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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206 #if str($tree_parameters.tree_topology.zb) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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207 -zb '$tree_parameters.tree_topology.zb'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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208 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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209
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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210 $tree_parameters.tree_topology.zw
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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211 $tree_parameters.tree_topology.au
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212
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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213 #if str($tree_parameters.constructing_consensus.minsup) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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214 -minsup '$tree_parameters.constructing_consensus.minsup'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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215 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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216
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217
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218 #if str($tree_parameters.generating_random.r) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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219 -r '$tree_parameters.generating_random.r'
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220 #end if
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221
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iuc
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222 $tree_parameters.generating_random.ru
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iuc
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223 $tree_parameters.generating_random.rcat
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iuc
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224 $tree_parameters.generating_random.rbal
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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225 $tree_parameters.generating_random.rcsg
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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226
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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227 #if str($tree_parameters.generating_random.rlen) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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228 -rlen '$tree_parameters.generating_random.rlen'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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229 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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230
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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231 #if str($bootstrap_parameters.ultrafast_bootstrap.bb) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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232 -bb '$bootstrap_parameters.ultrafast_bootstrap.bb'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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233 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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234
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iuc
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235 $bootstrap_parameters.ultrafast_bootstrap.wbt
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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236 $bootstrap_parameters.ultrafast_bootstrap.wbtl
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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237
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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238 #if str($bootstrap_parameters.ultrafast_bootstrap.nm) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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239 -nm '$bootstrap_parameters.ultrafast_bootstrap.nm'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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240 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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241
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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242 #if str($bootstrap_parameters.ultrafast_bootstrap.bcor) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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243 -bcor '$bootstrap_parameters.ultrafast_bootstrap.bcor'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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244 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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245
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246 #if str($bootstrap_parameters.ultrafast_bootstrap.nstep) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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247 -nstep '$bootstrap_parameters.ultrafast_bootstrap.nstep'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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248 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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249
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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250 #if str($bootstrap_parameters.ultrafast_bootstrap.beps) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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251 -beps '$bootstrap_parameters.ultrafast_bootstrap.beps'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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252 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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253
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254 #if str($bootstrap_parameters.ultrafast_bootstrap.bspec) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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255 -bspec '$bootstrap_parameters.ultrafast_bootstrap.bspec'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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256 #end if
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257
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258 $bootstrap_parameters.ultrafast_bootstrap.bnni
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259
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260 #if str($bootstrap_parameters.nonparametric_bootstrap.b) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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261 -b '$bootstrap_parameters.nonparametric_bootstrap.b'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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262 #end if
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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263
0
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264 $bootstrap_parameters.nonparametric_bootstrap.bc
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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265 $bootstrap_parameters.nonparametric_bootstrap.bo
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266
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267 #if str($miscellaneous_options.fconst) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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268 -fconst '$miscellaneous_options.fconst'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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269 #end if
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270
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271 ]]>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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272 </command>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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273 <inputs>
1
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274 <section name="general_options" expanded="True" title="General options">
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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275 <param argument="-s" type="data" format="txt" optional="true" label="Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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276 <param argument="-st" type="select" label="Specify sequence type as either of DNA, AA, BIN, MORPH, CODON or NT2AA for DNA, amino-acid, binary, morphological, codon or DNA-to-AA-translated sequences">
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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277 <help><![CDATA[
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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278 Note that -st CODON is always necessary when using codon models and you also need to specify a genetic code like this if differed from the standard genetic code.
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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279 <br/><i>-st</i> NT2AA tells IQ-TREE to translate protein-coding DNA into AA sequences and then subsequent analysis will work on the AA sequences. You can also use a genetic code like -st NT2AA5 for the Invertebrate Mitochondrial Code (see genetic code table).]]>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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280 </help>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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281 <option value="DNA">DNA</option>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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282 <option value="AA">AA</option>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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283 <option value="BIN">BIN</option>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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284 <option value="MORPH">MORPH</option>
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285 <option value="CODON">CODON</option>
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286 <option value="NT2AA">NT2AA</option>
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287 </param>
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288 <param argument="-t" type="data" format="nhx" optional="true" label="Specify a file containing starting tree for tree search"/>
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289 <param argument="-te" type="data" format="nhx" optional="true" label="Like -t but fixing user tree" help="That means, no tree search is performed and IQ-TREE computes the log-likelihood of the fixed user tree."/>
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290 <param argument="-seed" type="integer" optional="true" label="Specify a random number seed to reproduce a previous run (leave blank to randomize)"/>
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291 <param argument="-keep_ident" type="boolean" truevalue="-keep-ident" falsevalue="" checked="false" label="Keep identical sequences in the alignment" help="By default: IQ-TREE will remove them during the analysis and add them in the end."/>
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292 <param argument="-safe" type="boolean" truevalue="-safe" falsevalue="" checked="false" label="Turn on safe numerical mode to avoid numerical underflow for large data sets with many sequences (typically in the order of thousands)" help="This mode is automatically turned on when having more than 2000 sequences."/>
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293 </section>
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294 <section name="likelihood_mapping" expanded="False" title="Likelihood mapping analysis">
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295 <param argument="-lmap" type="integer" optional="true" label="Specify the number of quartets to be randomly drawn" help="If you specify -lmap ALL, all unique quartets will be drawn, instead."/>
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296 <param argument="-lmclust" type="data" format="txt" optional="true" label="Specify a NEXUS file containing taxon clusters (see below for example) for quartet mapping analysis."/>
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297 <param argument="-wql" type="boolean" truevalue="-wql" falsevalue="" checked="false" label="Write quartet log-likelihoods into .lmap.quartetlh file (typically not needed)."/>
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298 </section>
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299 <section name="modelling_parameters" title="Modelling Parameters">
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300 <section name="automatic_model" expanded="False" title="Automatic model selection">
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301 <conditional name="cond_model" >
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302 <param name="opt_custommodel" type="boolean" checked="false" label="Use Custom Model" help="See http://www.iqtree.org/doc/Substitution-Models"/>
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303 <when value="true">
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304 <param argument="-m" type="text" label="Model">
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305 <sanitizer>
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306 <valid initial="string.ascii_uppercase,+" />
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307 </sanitizer>
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308 </param>
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309 </when>
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310 <when value="false">
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311 <param argument="-m" type="select" label="Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein)" >
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312 <help><![CDATA[
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313 <b>Note:</b> Only <code>TEST</code> and custom models that do not rely on <code>MF</code> can be used in conjunction with bootstrap parameters (-b)<br/><br/>
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314 IQ-TREE also works for codon, binary and morphogical data.
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315 <table>
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316 <tr>
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317 <td><i>TESTONLY</i></td>
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318 <td>Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein). Moreover, IQ-TREE also works for codon, binary and morphogical data.</td>
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319 </tr>
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320 <tr>
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321 <td><i>TEST</i></td>
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322 <td>Like -m TESTONLY but immediately followed by tree reconstruction using the best-fit model found. So this performs both model selection and tree inference within a single run.</td>
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323 </tr>
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324 <tr>
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325 <td><i>TESTNEWONLY</i></td>
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326 <td>Perform an extended model selection that additionally includes FreeRate model compared with -m TESTONLY. Recommended as replacement for -m TESTONLY. Note that LG4X is a FreeRate model, but by default is not included because it is also a protein mixture model. To include it, use -madd option (see table below).</td>
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327 </tr>
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328 <tr>
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329 <td><i>TESTNEW</i></td>
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330 <td>Like -m MF but immediately followed by tree reconstruction using the best-fit model found.</td>
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331 </tr>
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332 <tr>
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333 <td><i>TESTMERGEONLY</i></td>
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334 <td>Select best-fit partitioning scheme like PartitionFinder.</td>
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335 </tr>
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336 <tr>
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337 <td><i>TESTMERGE</i></td>
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338 <td>Like -m TESTMERGEONLY but immediately followed by tree reconstruction using the best partitioning scheme found.</td>
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339 </tr>
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340 <tr>
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341 <td><i>TESTNEWMERGEONLY</i></td>
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342 <td>Like -m TESTMERGEONLY but additionally includes FreeRate model.</td>
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343 </tr>
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344 <tr>
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345 <td><i>TESTNEWMERGE</i></td>
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346 <td>Like -m MF+MERGE but immediately followed by tree reconstruction using the best partitioning scheme found.</td>
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347 </tr>
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348 </table>
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349 ]]>
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350 </help>
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351 <option value="" selected="true">(None)</option>
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352 <option value="TESTONLY">TESTONLY</option>
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353 <option value="TEST">TEST</option>
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354 <option value="TESTNEWONLY">TESTNEWONLY</option>
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355 <option value="TESTNEW">TESTNEW</option>
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356 <option value="TESTMERGEONLY">TESTMERGEONLY</option>
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357 <option value="TESTMERGE">TESTMERGE</option>
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358 <option value="TESTNEWMERGEONLY">TESTNEWMERGEONLY</option>
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359 <option value="TESTNEWMERGE">TESTNEWMERGE</option>
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360 </param>
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361 </when>
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362 </conditional>
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363 <param argument="-rcluster" type="integer" optional="true" label="Specify the percentage for the relaxed clustering algorithm (Lanfear et al., 2014)" help="This is similar to --rcluster-percent option of PartitionFinder. For example, with -rcluster 10 only the top 10% partition schemes are considered to save computations." />
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364 <param argument="-mset" type="text" optional="true" label="Specify the name of a program (raxml, phyml or mrbayes) to restrict to only those models supported by the specified program" help="Alternatively, one can specify a comma-separated list of base models. For example, -mset WAG,LG,JTT will restrict model selection to WAG, LG, and JTT instead of all 18 AA models to save computations.">
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365 <sanitizer>
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366 <valid initial="string.ascii_uppercase,string.punctuation" />
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367 </sanitizer>
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368 </param>
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369 <param argument="-msub" type="select" label="Specify either nuclear, mitochondrial, chloroplast or viral to restrict to those AA models designed for specified source." help="">
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370 <option value="nuclear">nuclear</option>
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371 <option value="mitochondrial">mitochondrial</option>
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372 <option value="chloroplast">chloroplast</option>
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373 <option value="viral">viral</option>
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374 </param>
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375 <param argument="-mfreq" type="text" optional="true" label="Specify a comma-separated list of frequency types for model selection" >
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376 <sanitizer>
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377 <valid initial="string.ascii_uppercase,string.digits,x,string.punctuation" />
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378 </sanitizer>
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379 </param>
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380 <param argument="-mrate" type="text" optional="true" label="Specify a comma-separated list of rate heterogeneity types for model selection">
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381 <sanitizer>
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382 <valid initial="string.ascii_uppercase,string.punctuation" />
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383 </sanitizer>
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384 </param>
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385 <param argument="-cmin" type="integer" value="2" optional="true" label="Specify minimum number of categories for FreeRate model"/>
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386 <param argument="-cmax" type="integer" value="10" optional="true" label="Specify maximum number of categories for FreeRate model"/>
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387 <param argument="-merit" type="select" label="Specify either AIC, AICc or BIC for the optimality criterion to apply for new procedure" help="">
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388 <option value="AIC">AIC</option>
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389 <option value="AICc">AICc</option>
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390 <option value="BIC">BIC</option>
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391 </param>
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392 <param argument="-mtree" type="boolean" truevalue="-mtree" falsevalue="" checked="false" label="Turn on full tree search for each model considered, to obtain more accurate result"/>
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393 <param argument="-madd" type="text" optional="true" label="Specify a comma-separated list of mixture models to additionally consider for model selection" help="For example, -madd LG4M,LG4X to additionally include these two protein mixture models.">
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394 <sanitizer>
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395 <valid initial="string.ascii_uppercase,string.digits,string.punctuation" />
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396 </sanitizer>
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397 </param>
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398 <param argument="-mdef" type="data" format="txt" optional="true" label="Specify a NEXUS model file to define new models."/>
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399 </section>
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400 <section name="specifying_substitution" expanded="False" title="Specifying substitution models">
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401 <param argument="-mwopt" type="boolean" truevalue="-mwopt" falsevalue="" checked="false" label="Turn on optimizing weights of mixture models" help="Note that for models like LG+C20+F+G this mode is automatically turned on, but not for LG+C20+G."/>
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402 </section>
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403 <section name="rate_heterogeneity" expanded="False" title="Rate heterogeneity">
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404 <param argument="-a" type="text" optional="true" label="Specify the Gamma shape parameter (default: estimate)">
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405 <sanitizer>
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406 <valid initial="string.printable" />
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407 </sanitizer>
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408 </param>
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409 <param argument="-gmedian" type="boolean" truevalue="-gmedian" falsevalue="" checked="false" label="Perform the median approximation for Gamma rate heterogeneity instead of the default mean approximation (Yang, 1994)"/>
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410 <param argument="-i" type="text" optional="true" label="Specify the proportion of invariable sites (default: estimate)">
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411 <sanitizer>
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412 <valid initial="string.printable" />
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413 </sanitizer>
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414 </param>
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415 <param argument="--opt_gamma_inv" type="boolean" truevalue="--opt-gamma-inv" falsevalue="" checked="false" label="Perform more thorough estimation for +I+G model parameters"/>
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416 <param argument="-wsr" type="boolean" truevalue="-wsr" falsevalue="" checked="false" label="Write per-site rates to .rate file"/>
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417 </section>
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418 <section name="partition_model" expanded="False" title="Partition model options">
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419 <param argument="-q" type="data" format="txt" optional="true" label="Specify partition file for edge-equal partition model" help="That means, all partitions share the same set of branch lengths (like -q option of RAxML)."/>
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420 <param argument="-spp" type="boolean" truevalue="-spp" falsevalue="" checked="false" label="Like -q but allowing partitions to have different evolutionary speeds (edge-proportional partition model)."/>
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421 <param argument="-sp" type="data" format="txt" optional="true" label="Specify partition file for edge-unlinked partition model" help="That means, each partition has its own set of branch lengths (like -M option of RAxML). This is the most parameter-rich partition model to accomodate heterotachy."/>
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422 </section>
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423 <section name="site_specific_frequency" expanded="False" title="Site-specific frequency model options">
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424 <param argument="-ft" type="data" format="nhx" optional="true" label="Specify a guide tree to infer site frequency profiles."/>
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425 <param argument="-fs" type="float" optional="true" label="Specify a site frequency file, e.g" help="the .sitefreq file obtained from -ft run. This will save memory used for the first phase of the analysis."/>
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426 <param argument="-fmax" type="boolean" truevalue="-fmax" falsevalue="" checked="false" label="Switch to posterior maximum mode for obtaining site-specific profiles" help="Default: posterior mean."/>
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427 </section>
1
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428 </section>
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429 <section name="tree_parameters" title="Tree Parameters">
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430 <section name="tree_search" expanded="False" title="Tree search parameters">
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431 <param argument="-n" type="integer" optional="true" label="Skip subsequent tree search (n = 0), useful when you only want to assess the phylogenetic information of the alignment. Otherwise specify number of iterations to stop (this option overrides -nstop criterion)." />
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432 <param argument="-ninit" type="integer" value="100" optional="true" label="Specify number of initial parsimony trees"/>
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433 <param argument="-ntop" type="integer" value="20" optional="true" label="Specify number of top initial parsimony trees to optimize with ML nearest neighbor interchange (NNI) search to initialize the candidate set"/>
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434 <param argument="-nbest" type="integer" value="5" optional="true" label="Specify number of trees in the candidate set to maintain during ML tree search"/>
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435 <param argument="-nstop" type="integer" value="100" optional="true" label="Specify number of unsuccessful iterations to stop"/>
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436 <param argument="-sprrad" type="integer" value="6" optional="true" label="Specify SPR radius for the initial parsimony tree search"/>
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437 <param argument="-pers" type="float" value="0.5" optional="true" label="Specify perturbation strength (between 0 and 1) for randomized NNI"/>
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438 <param argument="-allnni" type="boolean" truevalue="-allnni" falsevalue="" checked="false" label="Turn on more thorough and slower NNI search"/>
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439 <param argument="-djc" type="boolean" truevalue="-djc" falsevalue="" checked="false" label="Avoid computing ML pairwise distances and BIONJ tree."/>
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440 <param argument="-g" type="data" format="txt" optional="true" label="Specify a topological constraint tree file in NEWICK format" help="The constraint tree can be a multifurcating tree and need not to include all taxa."/>
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441 </section>
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442 <section name="single_branch" expanded="False" title="Single branch tests">
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443 <param argument="-alrt" type="integer" optional="true" label="Specify number of replicates (&gt;=1000) to perform SH-like approximate likelihood ratio test (SH-aLRT) (Guindon et al., 2010)" help="If number of replicates is set to 0 (-alrt 0), then the parametric aLRT test (Anisimova and Gascuel 2006) is performed, instead of SH-aLRT."/>
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444 <param argument="-abayes" type="boolean" truevalue="-abayes" falsevalue="" checked="false" label="Perform approximate Bayes test (Anisimova et al., 2011)."/>
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445 <param argument="-lbp" type="integer" optional="true" label="Specify number of replicates (&gt;=1000) to perform fast local bootstrap probability method (Adachi and Hasegawa, 1996)."/>
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446 </section>
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447 <section name="tree_topology" expanded="False" title="Tree topology tests">
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448 <param argument="-z" type="data" format="txt" optional="true" label="Specify a file containing a set of trees" help="IQ-TREE will compute the log-likelihoods of all trees."/>
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449 <param argument="-zb" type="integer" optional="true" label="Specify the number of RELL (Kishino et al., 1990) replicates (&gt;=1000) to perform several tree topology tests for all trees passed via -z" help="The tests include bootstrap proportion (BP), KH test (Kishino and Hasegawa, 1989), SH test (Shimodaira and Hasegawa, 1999) and expected likelihood weights (ELW) (Strimmer and Rambaut, 2002)."/>
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450 <param argument="-zw" type="boolean" truevalue="-zw" falsevalue="" checked="false" label="Used together with -zb to additionally perform the weighted-KH and weighted-SH tests."/>
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451 <param argument="-au" type="boolean" truevalue="-au" falsevalue="" checked="false" label="Used together with -zb to additionally perform the approximately unbiased (AU) test (Shimodaira, 2002)" help="Note that you have to specify the number of replicates for the AU test via -zb."/>
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452 </section>
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453 <section name="constructing_consensus" expanded="False" title="Constructing consensus tree">
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454 <param argument="-con" type="boolean" truevalue="-con" falsevalue="" checked="false" label="Compute consensus tree of the trees passed via -t" help="Resulting consensus tree is written to .contree file."/>
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455 <param argument="-net" type="boolean" truevalue="-net" falsevalue="" checked="false" label="Compute consensus network of the trees passed via -t" help="Resulting consensus network is written to .nex file."/>
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456 <param argument="-minsup" type="float" value="0.0" optional="true" label="Specify a minimum threshold (between 0 and 1) to keep branches in the consensus tree"/>
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457 <param argument="-bi" type="integer" optional="true" label="Specify a burn-in, which is the number of beginning trees passed via -t to discard before consensus construction" help="This is useful e.g. when summarizing trees from MrBayes analysis."/>
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458 <param argument="-sup" type="data" format="nhx" optional="true" label="Specify an input “target” tree file" help="That means, support values are first extracted from the trees passed via -t, and then mapped onto the target tree. Resulting tree with assigned support values is written to .suptree file. This option is useful to map and compare support values from different approaches onto a single tree."/>
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459 <param argument="-suptag" type="text" optional="true" label="Specify name of a node in -sup target tree" help="The corresponding node of .suptree will then be assigned with IDs of trees where this node appears. Special option -suptag ALL will assign such IDs for all nodes of the target tree."/>
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460 </section>
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461 <section name="computing_robinson_foulds" expanded="False" title="Computing Robinson-Foulds distance">
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462 <param argument="-rf" type="data" format="nhx" optional="true" label="Specify a second set of trees" help="IQ-TREE computes all pairwise RF distances between two tree sets passed via -t and -rf"/>
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463 <param argument="-rf_all" type="boolean" truevalue="-rf_all" falsevalue="" checked="false" label="Compute all-to-all RF distances between all trees passed via -t"/>
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464 <param argument="-rf_adj" type="boolean" truevalue="-rf_adj" falsevalue="" checked="false" label="Compute RF distances between adjacent trees passed via -t"/>
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465 </section>
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466 <section name="generating_random" expanded="False" title="Generating random trees">
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467 <param argument="-r" type="integer" optional="true" label="Specify number of taxa" help="IQ-TREE will create a random tree under Yule-Harding model with specified number of taxa"/>
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468 <param argument="-ru" type="boolean" truevalue="-ru" falsevalue="" checked="false" label="Like -r, but a random tree is created under uniform model."/>
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469 <param argument="-rcat" type="boolean" truevalue="-rcat" falsevalue="" checked="false" label="Like -r, but a random caterpillar tree is created."/>
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470 <param argument="-rbal" type="boolean" truevalue="-rbal" falsevalue="" checked="false" label="Like -r, but a random balanced tree is created."/>
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471 <param argument="-rcsg" type="boolean" truevalue="-rcsg" falsevalue="" checked="false" label="Like -r, bur a random circular split network is created."/>
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472 <param argument="-rlen" type="text" optional="true" label="Specify three numbers: minimum, mean and maximum branch lengths of the random tree">
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473 <sanitizer>
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474 <valid initial="string.digits,string.whitespace" />
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475 </sanitizer>
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476 </param>
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477 </section>
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478 </section>
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479 <section name="bootstrap_parameters" title="Bootstrap Parameters">
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480 <section name="ultrafast_bootstrap" expanded="False" title="Ultrafast bootstrap parameters">
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481 <param argument="-bb" type="integer" optional="true" label="Specify number of bootstrap replicates (&gt;=1000)."/>
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482 <param argument="-wbt" type="boolean" truevalue="-wbt" falsevalue="" checked="false" label="Turn on writing bootstrap trees to .ufboot file"/>
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483 <param argument="-wbtl" type="boolean" truevalue="-wbtl" falsevalue="" checked="false" label="Like -wbt but bootstrap trees written with branch lengths"/>
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484 <param argument="-nm" type="integer" value="1000" optional="true" label="Specify maximum number of iterations to stop"/>
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485 <param argument="-bcor" type="float" value="0.99" optional="true" label="Specify minimum correlation coefficient for UFBoot convergence criterion"/>
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486 <param argument="-nstep" type="integer" value="100" optional="true" label="Specify iteration interval checking for UFBoot convergence"/>
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487 <param argument="-beps" type="float" value="0.5" optional="true" label="Specify a small epsilon to break tie in RELL evaluation for bootstrap trees"/>
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488 <param argument="-bspec" type="text" optional="true" label="Specify the resampling strategies for partitioned analysis" help="By default, IQ-TREE resamples alignment sites within partitions. With -bspec GENE IQ-TREE will resample partitions. With -bspec GENESITE IQ-TREE will resample partitions and then resample sites within resampled partitions (Gadagkar et al., 2005).">
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489 <sanitizer>
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490 <valid initial="string.ascii_uppercase" />
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491 </sanitizer>
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492 </param>
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493 <param argument="-bnni" type="boolean" truevalue="-bnni" falsevalue="" checked="false" label="Perform an additional step to further optimize UFBoot trees by nearest neighbor interchange (NNI) based directly on bootstrap alignments" help="This option is recommended in the presence of severe model violations. It increases computing time by 2-fold but reduces the risk of overestimating branch supports due to severe model violations. Introduced in IQ-TREE 1.6."/>
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494 </section>
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495 <section name="nonparametric_bootstrap" expanded="False" title="Nonparametric bootstrap">
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496 <param argument="-b" type="integer" optional="true" label="Specify number of bootstrap replicates (recommended &gt;=100)" help="This will perform both bootstrap and analysis on original alignment and provide a consensus tree."/>
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497 <param argument="-bc" type="boolean" truevalue="-bc" falsevalue="" checked="false" label="Like -b but omit analysis on original alignment."/>
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498 <param argument="-bo" type="boolean" truevalue="-bo" falsevalue="" checked="false" label="Like -b but only perform bootstrap analysis (no analysis on original alignment and no consensus tree)."/>
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499 </section>
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500 </section>
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501 <section name="miscellaneous_options" expanded="False" title="Miscellaneous options">
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502 <param argument="-fconst" type="text" optional="true" label="Specify a list of comma-separated integer numbers" help="The number of entries should be equal to the number of states in the model (e.g. 4 for DNA and 20 for protein). IQ-TREE will then add a number of constant sites accordingly. For example, -fconst 10,20,15,40 will add 10 constant sites of all A, 20 constant sites of all C, 15 constant sites of all G and 40 constant sites of all T into the alignment.">
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503 <sanitizer>
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504 <valid initial="string.digits,string.punctuation" />
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505 </sanitizer>
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506 </param>
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507 </section>
0
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508 </inputs>
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509 <outputs>
1
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510 <data name='bionj' format='nhx' from_work_dir="*.bionj" label="${tool.name} on ${on_string}: BIONJ Tree" />
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511 <data name='treefile' format='nhx' from_work_dir="*.treefile" label="${tool.name} on ${on_string}: MaxLikelihood Tree" />
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512 <data name='contree' format='nhx' from_work_dir="*.contree" label="${tool.name} on ${on_string}: Consensus Tree" />
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513 <data name='mldist' format='mldist' from_work_dir="*.mldist" label="${tool.name} on ${on_string}: MaxLikelihood Distance Matrix"/>
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514 <data name='splits.nex' format='nex' from_work_dir="*.splits.nex" label="${tool.name} on ${on_string}: Occurence Frequencies in Bootstrap Trees" />
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515 <data name='iqtree' format='iqtree' from_work_dir="*.iqtree" label="${tool.name} on ${on_string}: Report and Final Tree" />
0
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516 </outputs>
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517 <tests>
1
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518 <test>
0
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519 <param name="seed" value="1257" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
520 <param name="st" value="AA" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
521 <param name="s" value="example.phy" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
522 <param name="m" value="TESTNEW" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
523 <param name="msub" value="nuclear" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
524 <param name="madd" value="LG4M,LG4X" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
525 <param name="merit" value="AICc" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
526 <param name="bb" value="1000" />
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
527 <output name='bionj'>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
528 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
529 <has_text_matching expression=".*Human.*Whale.*" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
530 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
531 </output>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
532 <output name='iqtree'>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
533 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
534 <has_text_matching expression="VT\+F\+R3(\s+((-|\d|\.)+))+" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
535 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
536 </output>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
537 <output name='mldist'>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
538 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
539 <has_line_matching expression="^Frog(\s+((\d|\.)+))+\s+$" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
540 <has_line_matching expression="^Whale(\s+((\d|\.)+))+\s+$" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
541 <has_line_matching expression="^Cow(\s+((\d|\.)+))+\s+$" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
542 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
543 </output>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
544 <output name='treefile'>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
545 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
546 <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
547 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
548 </output>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
549 <output name='contree' >
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
550 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
551 <has_line_matching
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
552 expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*\)\d+:(\d|\.)+,.*" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
553 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
554 </output>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
555 <output name='splits.nex'>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
556 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
557 <has_line line="BEGIN Splits;" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
558 <has_line line="END; [Splits]" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
559 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
560 </output>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
561 </test>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
562 <test>
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
563 <!-- bootstrap sans model -->
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
564 <param name="seed" value="1257" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
565 <param name="st" value="AA" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
566 <param name="s" value="example.phy" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
567 <!-- <param name="m" value="TESTONLY" /> -->
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
568 <param name="msub" value="nuclear" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
569 <param name="cmin" value="2" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
570 <param name="cmax" value="10" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
571 <param name="merit" value="AICc" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
572 <param name="madd" value="LG4M,LG4X" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
573 <param name="ninit" value="100" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
574 <param name="ntop" value="20" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
575 <param name="nbest" value="5" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
576 <param name="nstop" value="100" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
577 <param name="sprrad" value="6" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
578 <param name="pers" value="0.5" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
579 <param name="minsup" value="0.0" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
580 <param name="nm" value="1000" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
581 <param name="bcor" value="0.99" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
582 <param name="nstep" value="100" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
583 <param name="beps" value="0.5" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
584 <param name="b" value="2" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
585 <output name='iqtree'>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
586 <assert_contents>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
587 <has_text_matching expression="VT\+F\+I(\s+((-|\d|\.)+))+" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
588 </assert_contents>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
589 </output>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
590 <output name='treefile'>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
591 <assert_contents>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
592 <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
593 </assert_contents>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
594 </output>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
595 </test>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
596 <test>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
597 <!-- model sans bootstrap -->
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
598 <param name="seed" value="1257" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
599 <param name="st" value="AA" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
600 <param name="s" value="example.phy" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
601 <param name="m" value="TESTONLY" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
602 <param name="msub" value="nuclear" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
603 <param name="cmin" value="2" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
604 <param name="cmax" value="10" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
605 <param name="merit" value="AICc" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
606 <param name="madd" value="LG4M,LG4X" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
607 <param name="ninit" value="100" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
608 <param name="ntop" value="20" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
609 <param name="nbest" value="5" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
610 <param name="nstop" value="100" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
611 <param name="sprrad" value="6" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
612 <param name="pers" value="0.5" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
613 <param name="minsup" value="0.0" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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diff changeset
614 <param name="nm" value="1000" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
615 <param name="bcor" value="0.99" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
616 <param name="nstep" value="100" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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diff changeset
617 <param name="beps" value="0.5" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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diff changeset
618 <!-- <param name="b" value="100" /> -->
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
619 <output name='iqtree'>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
620 <assert_contents>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
621 <has_text_matching expression="VT\+F\+I(\s+((-|\d|\.)+))+" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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622 </assert_contents>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
623 </output>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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624 <output name='treefile'>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
625 <assert_contents>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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626 <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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627 </assert_contents>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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diff changeset
628 </output>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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diff changeset
629 </test>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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630 <test>
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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631 <param name='s' value='example.phy' />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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632 <output name='iqtree'>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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633 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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634 <has_text_matching expression=".*Human.*Whale.*" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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635 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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636 </output>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
637 <output name='treefile'>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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638 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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639 <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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640 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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641 </output>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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642 </test>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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643 </tests>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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644 <help>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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645 IQ-TREE
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
646 =======
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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647
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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648 The full documentation can be found here_.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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649
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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650 .. _here : http://www.iqtree.org/doc/
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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651
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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652 General Tutorial
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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653 ===================
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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654
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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655 Input data
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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656 ----------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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657
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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658 IQ-TREE takes as input a *multiple sequence alignment* and will reconstruct an evolutionary tree that is best explained by the input data. The input alignment can be in various common formats. For example the PHYLIP_ format which may look like:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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659
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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660 .. _PHYLIP: http://evolution.genetics.washington.edu/phylip/doc/sequence.html
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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661
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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662 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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663
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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664 7 28
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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665 Frog AAATTTGGTCCTGTGATTCAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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666 Turtle CTTCCACACCCCAGGACTCAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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667 Bird CTACCACACCCCAGGACTCAGCAGTAAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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668 Human CTACCACACCCCAGGAAACAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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669 Cow CTACCACACCCCAGGAAACAGCAGTGAC
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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670 Whale CTACCACGCCCCAGGACACAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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671 Mouse CTACCACACCCCAGGACTCAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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672
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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673 This tiny alignment contains 7 DNA sequences from several animals with the sequence length of 28 nucleotides. IQ-TREE also supports other file formats such as FASTA, NEXUS, CLUSTALW. The FASTA file for the above example may look like this:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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674
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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675 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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676
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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677 >Frog
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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678 AAATTTGGTCCTGTGATTCAGCAGTGAT
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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diff changeset
679 >Turtle
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
680 CTTCCACACCCCAGGACTCAGCAGTGAT
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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diff changeset
681 >Bird
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
682 CTACCACACCCCAGGACTCAGCAGTAAT
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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parents: 0
diff changeset
683 >Human
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
684 CTACCACACCCCAGGAAACAGCAGTGAT
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
685 >Cow
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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686 CTACCACACCCCAGGAAACAGCAGTGAC
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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diff changeset
687 >Whale
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
688 CTACCACGCCCCAGGACACAGCAGTGAT
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
689 >Mouse
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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690 CTACCACACCCCAGGACTCAGCAGTGAT
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
691
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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692 **NOTE**: If you have raw sequences, you need to first apply alignment programs like MAFFT_ or ClustalW_ to align the sequences, before feeding them into IQ-TREE.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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693
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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694 .. _MAFFT: http://mafft.cbrc.jp/alignment/software/
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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695 .. _ClustalW: http://www.clustal.org
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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696
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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697
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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698 Running example
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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699 ---------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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700
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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701 From the download_ there is an example alignment called `example.phy`
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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702 in PHYLIP format. This example contains parts of the mitochondrial DNA sequences of several animals (Source: `Phylogenetic Handbook`_)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
703
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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704 .. _`Phylogenetic Handbook` : http://www.kuleuven.be/aidslab/phylogenybook/home.html)).
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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parents:
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705 .. _download: http://www.iqtree.org/#download
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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706
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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707 You can now start to reconstruct a maximum-likelihood tree
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
708 from this alignment by entering (assuming that you are now in the same folder with `example.phy`):
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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parents:
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709
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
710 ::iqtree -s example.phy -st AA -seed 9999 -m TESTNEW -msub nuclear -madd LG4M,LG4x -merit AICc -bb 2000
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
711
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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parents:
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712 * **-s** is the option to specify the name of the alignment file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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713
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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714 * **-st** specifies the sequence type as amino-acid
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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parents:
diff changeset
715
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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716 * **-seed** ensures that the output files remain the same for subsequent runs
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
717
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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718 * **-m** sets the modelling parameter for standard model selection
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
719
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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720 * **-msub** determines the type sub-modelling
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
721
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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722 * **-madd** provides an additional selection mixed models
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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723
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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parents:
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724 * **-merit** asserts the type of optimality criterion
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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725
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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726 * **-bb** defines the number of replicates
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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parents: 0
diff changeset
727
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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parents:
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728
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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729 Each of these parameters are available under the relevant sub-sections in the main tool interface.
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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730
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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731 At the end of the run IQ-TREE will write several output files including:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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732
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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parents:
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733 * **example.phy.iqtree**: the main report file that is self-readable. You should look at this file to see the computational results. It also contains a textual representation of the final tree (see below).
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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734
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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735 * **example.phy.treefile**: the ML tree in NEWICK format, which can be visualized by any supported tree viewer programs like FigTree or iTOL.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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736
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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737 **NOTE**: Starting with version 1.5.4, with this simple command IQ-TREE will by default perform ModelFinder to find the best-fit substitution model and then infer a phylogenetic tree using the selected model.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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738
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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739 For this example data the resulting maximum-likelihood tree may look like this (extracted from **.iqtree** file):
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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740
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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741 **NOTE**: Tree is UNROOTED although outgroup taxon 'LngfishAu' is drawn at root
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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742
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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743 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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744
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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745 +--------------LngfishAu
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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746 |
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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747 | +--------------LngfishSA
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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748 +--------|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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749 | +--------------LngfishAf
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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750 |
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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751 | +-------------------Frog
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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752 +------|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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753 | +-----------------Turtle
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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754 | +-----|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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755 | | | +-----------------------Sphenodon
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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756 | | | +--|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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757 | | | | +--------------------------Lizard
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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758 | | +---|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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759 | | | +---------------------Crocodile
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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760 | | +------|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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761 | | +------------------Bird
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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762 +---------|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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763 | +----------------Human
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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764 | +--|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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765 | | | +--------Seal
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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766 | | +--|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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767 | | | +-------Cow
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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768 | | +---|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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769 | | +---------Whale
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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770 | +----|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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771 | | | +------Mouse
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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772 | | +---------|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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773 | | +--------Rat
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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774 +----------|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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775 | +----------------Platypus
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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776 +---|
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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777 +-------------Opossum
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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778
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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779
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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780 This makes sense as the mammals (**Human** to **Opossum**) form a clade, whereas the reptiles **Turtle** to **Crocodile**) and **Bird** form a separate sister clade. Here the tree is drawn at the *outgroup* Lungfish which is more accient than other species in this example. However, please note that IQ-TREE always produces an **unrooted tree** as it knows nothing about this biological background; IQ-TREE simply draws the tree this way as **LngfishAu** is the first sequence occuring in the alignment.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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781
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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782 Choosing the right substitution model
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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783 -------------------------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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784
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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785 IQ-TREE will choose the best model for you automatically if specify any of the TEST models, but valid custom models can also be specified that conform to those found in Models_ page.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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786
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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787 .. _Models: http://www.iqtree.org/doc/Substitution-Models#binary-and-morphological-models
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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788
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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789
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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790 ------------------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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791
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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792 Advanced Parameter Selection
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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793 ============================
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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794
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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795 Using codon models
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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796 ------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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797
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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798 IQ-TREE supports a number of codon models. You need to input a protein-coding DNA alignment and specify codon data by option **-st CODON** (Otherwise, IQ-TREE applies DNA model because it detects that your alignment has DNA sequences):
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
799
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
800 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
801
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
802 iqtree -s coding_gene.phy -st CODON
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
803
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
804 If your alignment length is not divisible by 3, IQ-TREE will stop with an error message. IQ-TREE will group sites 1,2,3 into codon site 1; sites 4,5,6 to codon site 2; etc. Moreover, any codon, which has at least one gap/unknown/ambiguous nucleotide, will be treated as unknown codon character.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
805
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
806 Note that the above command assumes the standard genetic code. If your sequences follow 'The Invertebrate Mitochondrial Code', then run:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
807
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
808 ::
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
809
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
810 iqtree -s coding_gene.phy -st CODON5
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
811
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
812 Note that ModelFinder works for codon alignments. IQ-TREE version >= 1.5.4 will automatically invokes ModelFinder to find the best-fit codon model.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
813
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
814
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
815 Assessing branch supports with ultrafast bootstrap approximation
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
816 ----------------------------------------------------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
817
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
818 To overcome the computational burden required by the nonparametric bootstrap, IQ-TREE introduces an ultrafast bootstrap approximation (UFBoot) ([Minh et al., 2013]) that is orders of magnitude faster than the standard procedure and provides relatively unbiased branch support values. Citation for UFBoot:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
819
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
820 B.Q. Minh, M.A.T. Nguyen, and A. von Haeseler (2013) Ultrafast approximation for phylogenetic bootstrap. _Mol. Biol. Evol., 30:1188-1195.
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
821
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
822 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
823
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
824 iqtree -s example.phy -m TIM2+I+G -bb 1000
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
825
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
826 **-bb** specifies the number of bootstrap replicates where 1000 is the minimum number recommended. The section **MAXIMUM LIKELIHOOD TREE** in **example.phy.iqtree** shows a textual representation of the maximum likelihood tree with branch support values in percentage. The NEWICK format of the tree is printed to the file **example.phy.treefile**. In addition, IQ-TREE writes the following files:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
827
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
828 * **example.phy.contree**: the consensus tree with assigned branch supports where branch lengths are optimized on the original alignment.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
829
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
830 * **example.phy.splits**: support values in percentage for all splits (bipartitions), computed as the occurence frequencies in the bootstrap trees. This file is in "star-dot" format.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
831
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
832 * **example.phy.splits.nex**: has the same information as **example.phy.splits** but in NEXUS format, which can be viewed with the program SplitsTree_ to explore the conflicting signals in the data. So it is more informative than consensus tree, e.g. you can see how highly supported the second best conflicting split is, which had no chance to enter the consensus tree.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
833
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
834 .. _SplitsTree: http://www.splitstree.org
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
835
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
836
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
837 Reducing impact of severe model violations with UFBoot
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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838 ------------------------------------------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
839
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
840 Starting with IQ-TREE version 1.6 we provide a new option **-bnni** to reduce the risk of overestimating branch supports with UFBoot due to severe model violations. With this option UFBoot will further optimize each bootstrap tree using a hill-climbing nearest neighbor interchange (NNI) search based directly on the corresponding bootstrap alignment.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
841
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
842 Thus, if severe model violations are present in the data set at hand, users are advised to append **-bnni** to the regular UFBoot command:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
843
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
844 iqtree -s example.phy -m TIM2+I+G -bb 1000 -bnni
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
845
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
846 For more details see:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
847
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
848 D.T. Hoang, O. Chernomor, A. von Haeseler, B.Q. Minh, L.S. Vinh (2017) UFBoot2: Improving the ultrafast bootstrap approximation.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
849
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
850
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
851 Assessing branch supports with standard nonparametric bootstrap
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
852 ----------------------------------------------------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
853
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
854 The standard nonparametric bootstrap is invoked by the **-b** option:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
855
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
856 iqtree -s example.phy -m TIM2+I+G -b 100
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
857
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
858 **-b** specifies the number of bootstrap replicates where 100
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
859 is the minimum recommended number. The output files are similar to those produced by the UFBoot procedure.
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
860
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
861
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
862
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
863 Assessing branch supports with single branch tests
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
864 --------------------------------------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
865
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
866 IQ-TREE provides an implementation of the SH-like approximate likelihood ratio test ([Guindon et al., 2010]). To perform this test, run:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
867
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
868 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
869
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
870 iqtree -s example.phy -m TIM2+I+G -alrt 1000
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
871
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
872 **-alrt** specifies the number of bootstrap replicates for SH-aLRT where 1000 is the minimum number recommended.
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
873
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
874 IQ-TREE also supports other tests such as the aBayes test (Anisimova et al., 2011) and the local bootstrap test (Adachi and Hasegawa, 1996).
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
875
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
876 You can also perform both SH-aLRT and the ultrafast bootstrap within one single run:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
877
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
878 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
879
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
880 iqtree -s example.phy -m TIM2+I+G -alrt 1000 -bb 1000
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
881
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
882 The branches of the resulting **.treefile** will be assigned with both SH-aLRT and UFBoot support values, which are readable by any tree viewer program like FigTree, Dendroscope or ETE. You can also look at the textual tree figure in **.iqtree** file:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
883
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
884 **NOTE**: Tree is UNROOTED although outgroup taxon 'LngfishAu' is drawn at root
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
885 Numbers in parentheses are SH-aLRT support (%) / ultrafast bootstrap support (%)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
886
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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887 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
888
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
889 +-------------LngfishAu
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
890 |
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
891 | +--------------LngfishSA
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
892 +-------| (100/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
893 | +------------LngfishAf
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
894 |
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
895 | +--------------------Frog
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
896 +------| (99.8/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
897 | +-----------------Turtle
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
898 | +--| (85/72)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
899 | | | +------------------------Crocodile
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
900 | | +----| (96.5/97)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
901 | | +------------------Bird
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
902 | +--| (39/51)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
903 | | +---------------------------Sphenodon
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
904 | +-----| (98.2/99)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
905 | | +-------------------------------Lizard
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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906 +---------| (100/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
907 | +--------------Human
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
908 | +--| (92.3/93)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
909 | | | +------Seal
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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910 | | +--| (68.3/75)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
911 | | | +-----Cow
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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912 | | +--| (99.7/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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913 | | +-------Whale
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
914 | +----| (99.1/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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915 | | | +---Mouse
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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916 | | +---------| (100/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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917 | | +------Rat
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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918 +-----------| (100/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
919 | +--------------Platypus
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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920 +--| (93/98)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
921 +-----------Opossum
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
922
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
923
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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924 From this figure, the branching patterns within reptiles are poorly supported (e.g. **Sphenodon** with SH-aLRT: 39%, UFBoot: 51% and **Turtle** with SH-aLRT: 85%, UFBoot: 72%) as well as the phylogenetic position of **Seal** within mammals (SH-aLRT: 68.3%, UFBoot: 75%). Other branches appear to be well supported.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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925 </help>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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926 <citations>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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927 <citation type="doi">10.1093/molbev/msu300</citation>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
928 <citation type="doi">10.1093/molbev/mst024</citation>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
929 </citations>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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930 </tool>