Mercurial > repos > iuc > iqtree

annotate iqtree.xml @ 3:973a28be3b7f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
author iuc
date Wed, 29 Jan 2020 16:34:20 -0500
parents d1c340a5664b
children f97743d52b87
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973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
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1 <tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@.3" >
0
05ee0a74faef 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>
2
d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
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3 <macros>
d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
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4 <import>iqtree_macros.xml</import>
d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
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5 </macros>
d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
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6 <expand macro="requirements" />
0
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iuc
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7 <command detect_errors='exit_code' ><![CDATA[
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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8 iqtree
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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9 -pre PREF
1
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10 -nt \${GALAXY_SLOTS:-10}
0
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11 -redo
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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12
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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13 ## file
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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14 #if $general_options.s
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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15 -s '$general_options.s'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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16 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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18 ## file
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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19 #if $general_options.t
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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20 -t '$general_options.t'
1
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21 $tree_parameters.constructing_consensus.con
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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22 $tree_parameters.constructing_consensus.net
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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23 #if str($tree_parameters.constructing_consensus.bi) != ''
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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24 -bi '$tree_parameters.constructing_consensus.bi'
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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25 #end if
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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27 ## file
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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28 #if $tree_parameters.constructing_consensus.sup
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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29 -sup '$tree_parameters.constructing_consensus.sup'
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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30 #end if
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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31
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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32 #if str($tree_parameters.constructing_consensus.suptag) != ''
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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33 -suptag '$tree_parameters.constructing_consensus.suptag'
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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34 #end if
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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36 ## file
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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37 #if $tree_parameters.computing_robinson_foulds.rf
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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38 -rf '$tree_parameters.computing_robinson_foulds.rf'
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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39 $tree_parameters.computing_robinson_foulds.rf_all
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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40 $tree_parameters.computing_robinson_foulds.rf_adj
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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41 #end if
0
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42 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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43
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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44 ## file
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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45 #if $general_options.te
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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46 -te '$general_options.te'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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47 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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48
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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49 #if str($general_options.st) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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50 -st '$general_options.st'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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51 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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53 #if str($general_options.seed) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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54 -seed '$general_options.seed'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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55 #end if
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56
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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57 $general_options.keep_ident
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58 $general_options.safe
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05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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60 #if str($likelihood_mapping.lmap) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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61 -lmap '$likelihood_mapping.lmap'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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62 #end if
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05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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64 ## file
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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65 #if $likelihood_mapping.lmclust
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66 -lmclust '$likelihood_mapping.lmclust'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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67 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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68
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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69 $likelihood_mapping.wql
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70
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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71 #if str($modelling_parameters.automatic_model.cond_model.m) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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72 -m '$modelling_parameters.automatic_model.cond_model.m'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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73 #end if
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74
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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75 #if str($modelling_parameters.automatic_model.rcluster) != ''
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76 -rcluster '$modelling_parameters.automatic_model.rcluster'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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77 #end if
1
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78
0
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79 #if str($modelling_parameters.automatic_model.mset) != ''
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80 -mset '$modelling_parameters.automatic_model.mset'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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81 #end if
1
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82
0
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83 #if str($modelling_parameters.automatic_model.msub) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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84 -msub '$modelling_parameters.automatic_model.msub'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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85 #end if
1
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86
0
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87 #if str($modelling_parameters.automatic_model.mfreq) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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88 -mfreq '$modelling_parameters.automatic_model.mfreq'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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89 #end if
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90
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91 #if str($modelling_parameters.automatic_model.mrate) != ''
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92 -mrate '$modelling_parameters.automatic_model.mrate'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
93 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
94
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
95 #if str($modelling_parameters.automatic_model.cmin) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
96 -cmin '$modelling_parameters.automatic_model.cmin'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
97 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
98
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
99 #if str($modelling_parameters.automatic_model.cmax) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
100 -cmax '$modelling_parameters.automatic_model.cmax'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
101 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
102
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
103 #if str($modelling_parameters.automatic_model.merit) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
104 -merit '$modelling_parameters.automatic_model.merit'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
105 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
106
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
107 $modelling_parameters.automatic_model.mtree
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
108
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
109 #if str($modelling_parameters.automatic_model.madd) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
110 -madd '$modelling_parameters.automatic_model.madd'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
111 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
112
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
113 ## file
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
114 #if $modelling_parameters.automatic_model.mdef
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
115 -mdef '$modelling_parameters.automatic_model.mdef'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
116 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
117
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
118 $modelling_parameters.specifying_substitution.mwopt
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
119
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
120 #if str($modelling_parameters.rate_heterogeneity.a) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
121 -a '$modelling_parameters.rate_heterogeneity.a'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
122 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
123
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
124 $modelling_parameters.rate_heterogeneity.gmedian
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
125
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
126 #if str($modelling_parameters.rate_heterogeneity.i) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
127 -i '$modelling_parameters.rate_heterogeneity.i'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
128 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
129
05ee0a74faef 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.opt_gamma_inv
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
131 $modelling_parameters.rate_heterogeneity.wsr
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
132
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
133 ## file
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
134 #if $modelling_parameters.partition_model.q
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
135 -q '$modelling_parameters.partition_model.q'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
136 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
137
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
138 $modelling_parameters.partition_model.spp
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
139
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
140 ## file
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
141 #if $modelling_parameters.partition_model.sp
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
142 -sp '$modelling_parameters.partition_model.sp'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
143 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
144
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
145 ## file
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
146 #if $modelling_parameters.site_specific_frequency.ft
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
147 -ft '$modelling_parameters.site_specific_frequency.ft'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
148 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
149
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
150 #if str($modelling_parameters.site_specific_frequency.fs) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
151 -fs '$modelling_parameters.site_specific_frequency.fs'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
152 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
153
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
154 $modelling_parameters.site_specific_frequency.fmax
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
155
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
156 #if str($tree_parameters.tree_search.ninit) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
157 -ninit '$tree_parameters.tree_search.ninit'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
158 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
159
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
160 #if str($tree_parameters.tree_search.ntop) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
161 -ntop '$tree_parameters.tree_search.ntop'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
162 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
163
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
164 #if str($tree_parameters.tree_search.nbest) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
165 -nbest '$tree_parameters.tree_search.nbest'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
166 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
167
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
168 #if str($tree_parameters.tree_search.nstop) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
169 -nstop '$tree_parameters.tree_search.nstop'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
170 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
171
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
172 #if str($tree_parameters.tree_search.n) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
173 -n '$tree_parameters.tree_search.n'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
174 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
175
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
176 #if str($tree_parameters.tree_search.sprrad) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
177 -sprrad '$tree_parameters.tree_search.sprrad'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
178 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
179
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
180 #if str($tree_parameters.tree_search.pers) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
181 -pers '$tree_parameters.tree_search.pers'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
182 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
183
05ee0a74faef 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.allnni
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
185 $tree_parameters.tree_search.djc
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
186
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
187 ## file
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
188 #if $tree_parameters.tree_search.g
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
189 -g '$tree_parameters.tree_search.g'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
190 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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191
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
192 #if str($tree_parameters.single_branch.alrt) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
193 -alrt '$tree_parameters.single_branch.alrt'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
194 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
195
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
196 $tree_parameters.single_branch.abayes
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
197
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
198 #if str($tree_parameters.single_branch.lbp) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
199 -lbp '$tree_parameters.single_branch.lbp'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
200 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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201
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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202 ## file
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
203 #if $tree_parameters.tree_topology.z
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
204 -z '$tree_parameters.tree_topology.z'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
205 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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206
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
207 #if str($tree_parameters.tree_topology.zb) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
208 -zb '$tree_parameters.tree_topology.zb'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
209 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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210
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
211 $tree_parameters.tree_topology.zw
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
212 $tree_parameters.tree_topology.au
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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213
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
214 #if str($tree_parameters.constructing_consensus.minsup) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
215 -minsup '$tree_parameters.constructing_consensus.minsup'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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216 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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217
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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218
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
219 #if str($tree_parameters.generating_random.r) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
220 -r '$tree_parameters.generating_random.r'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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221 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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222
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
223 $tree_parameters.generating_random.ru
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
224 $tree_parameters.generating_random.rcat
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
225 $tree_parameters.generating_random.rbal
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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226 $tree_parameters.generating_random.rcsg
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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227
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
228 #if str($tree_parameters.generating_random.rlen) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
229 -rlen '$tree_parameters.generating_random.rlen'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
230 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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231
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
232 #if str($bootstrap_parameters.ultrafast_bootstrap.bb) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
233 -bb '$bootstrap_parameters.ultrafast_bootstrap.bb'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
234 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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235
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
236 $bootstrap_parameters.ultrafast_bootstrap.wbt
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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237 $bootstrap_parameters.ultrafast_bootstrap.wbtl
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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238
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
239 #if str($bootstrap_parameters.ultrafast_bootstrap.nm) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
240 -nm '$bootstrap_parameters.ultrafast_bootstrap.nm'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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241 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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242
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
243 #if str($bootstrap_parameters.ultrafast_bootstrap.bcor) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
244 -bcor '$bootstrap_parameters.ultrafast_bootstrap.bcor'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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245 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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246
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
247 #if str($bootstrap_parameters.ultrafast_bootstrap.nstep) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
248 -nstep '$bootstrap_parameters.ultrafast_bootstrap.nstep'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
249 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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250
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
251 #if str($bootstrap_parameters.ultrafast_bootstrap.beps) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
252 -beps '$bootstrap_parameters.ultrafast_bootstrap.beps'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
253 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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254
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
255 #if str($bootstrap_parameters.ultrafast_bootstrap.bspec) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
256 -bspec '$bootstrap_parameters.ultrafast_bootstrap.bspec'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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257 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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258
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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259 $bootstrap_parameters.ultrafast_bootstrap.bnni
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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260
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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261 #if str($bootstrap_parameters.nonparametric_bootstrap.b) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
262 -b '$bootstrap_parameters.nonparametric_bootstrap.b'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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263 #end if
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
264
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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265 $bootstrap_parameters.nonparametric_bootstrap.bc
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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266 $bootstrap_parameters.nonparametric_bootstrap.bo
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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267
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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268 #if str($miscellaneous_options.fconst) != ''
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
269 -fconst '$miscellaneous_options.fconst'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
270 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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271
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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272 ]]>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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273 </command>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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274 <inputs>
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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diff changeset
275 <section name="general_options" expanded="True" title="General options">
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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276 <param argument="-s" type="data" format="txt" optional="true" label="Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format."/>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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277 <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
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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diff changeset
278 <help><![CDATA[
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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279 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
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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diff changeset
280 <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).]]>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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diff changeset
281 </help>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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diff changeset
282 <option value="DNA">DNA</option>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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283 <option value="AA">AA</option>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
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284 <option value="BIN">BIN</option>
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285 <option value="MORPH">MORPH</option>
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286 <option value="CODON">CODON</option>
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287 <option value="NT2AA">NT2AA</option>
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288 </param>
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289 <param argument="-t" type="data" format="nhx" optional="true" label="Specify a file containing starting tree for tree search"/>
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290 <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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291 <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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292 <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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293 <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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294 </section>
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295 <section name="likelihood_mapping" expanded="False" title="Likelihood mapping analysis">
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296 <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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297 <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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298 <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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299 </section>
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300 <section name="modelling_parameters" title="Modelling Parameters">
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301 <section name="automatic_model" expanded="False" title="Automatic model selection">
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302 <conditional name="cond_model" >
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303 <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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304 <when value="true">
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305 <param argument="-m" type="text" label="Model">
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306 <expand macro="sanitize_query"
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307 validinitial="string.ascii_uppercase,string.digits,string.punctuation" />
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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 <expand macro="sanitize_query"
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366 validinitial="string.ascii_uppercase,string.punctuation" />
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367 </param>
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368 <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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369 <option value="nuclear">nuclear</option>
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370 <option value="mitochondrial">mitochondrial</option>
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371 <option value="chloroplast">chloroplast</option>
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372 <option value="viral">viral</option>
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373 </param>
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374 <param argument="-mfreq" type="text" optional="true" label="Specify a comma-separated list of frequency types for model selection" >
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375 <expand macro="sanitize_query"
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376 validinitial="string.ascii_uppercase,string.digits,x,string.punctuation" />
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377 </param>
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378 <param argument="-mrate" type="text" optional="true" label="Specify a comma-separated list of rate heterogeneity types for model selection">
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379 <expand macro="sanitize_query"
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380 validinitial="string.ascii_uppercase,string.punctuation" />
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381 </param>
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382 <param argument="-cmin" type="integer" value="2" optional="true" label="Specify minimum number of categories for FreeRate model"/>
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383 <param argument="-cmax" type="integer" value="10" optional="true" label="Specify maximum number of categories for FreeRate model"/>
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384 <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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385 <option value="AIC">AIC</option>
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386 <option value="AICc">AICc</option>
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387 <option value="BIC">BIC</option>
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388 </param>
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389 <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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390 <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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391 <expand macro="sanitize_query"
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392 validinitial="string.ascii_uppercase,string.digits,string.punctuation" />
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393 </param>
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394 <param argument="-mdef" type="data" format="txt" optional="true" label="Specify a NEXUS model file to define new models."/>
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395 </section>
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396 <section name="specifying_substitution" expanded="False" title="Specifying substitution models">
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397 <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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398 </section>
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399 <section name="rate_heterogeneity" expanded="False" title="Rate heterogeneity">
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400 <param argument="-a" type="text" optional="true" label="Specify the Gamma shape parameter (default: estimate)">
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401 <expand macro="sanitize_query" />
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402 </param>
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403 <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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404 <param argument="-i" type="text" optional="true" label="Specify the proportion of invariable sites (default: estimate)">
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405 <expand macro="sanitize_query" />
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406 </param>
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407 <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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408 <param argument="-wsr" type="boolean" truevalue="-wsr" falsevalue="" checked="false" label="Write per-site rates to .rate file"/>
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409 </section>
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410 <section name="partition_model" expanded="False" title="Partition model options">
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411 <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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412 <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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413 <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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414 </section>
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415 <section name="site_specific_frequency" expanded="False" title="Site-specific frequency model options">
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416 <param argument="-ft" type="data" format="nhx" optional="true" label="Specify a guide tree to infer site frequency profiles."/>
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417 <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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418 <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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419 </section>
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420 </section>
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421 <section name="tree_parameters" title="Tree Parameters">
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422 <section name="tree_search" expanded="False" title="Tree search parameters">
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423 <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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424 <param argument="-ninit" type="integer" value="100" optional="true" label="Specify number of initial parsimony trees"/>
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425 <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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426 <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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427 <param argument="-nstop" type="integer" value="100" optional="true" label="Specify number of unsuccessful iterations to stop"/>
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428 <param argument="-sprrad" type="integer" value="6" optional="true" label="Specify SPR radius for the initial parsimony tree search"/>
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429 <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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430 <param argument="-allnni" type="boolean" truevalue="-allnni" falsevalue="" checked="false" label="Turn on more thorough and slower NNI search"/>
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431 <param argument="-djc" type="boolean" truevalue="-djc" falsevalue="" checked="false" label="Avoid computing ML pairwise distances and BIONJ tree."/>
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432 <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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433 </section>
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434 <section name="single_branch" expanded="False" title="Single branch tests">
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435 <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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436 <param argument="-abayes" type="boolean" truevalue="-abayes" falsevalue="" checked="false" label="Perform approximate Bayes test (Anisimova et al., 2011)."/>
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437 <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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438 </section>
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439 <section name="tree_topology" expanded="False" title="Tree topology tests">
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440 <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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441 <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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442 <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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443 <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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444 </section>
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445 <section name="constructing_consensus" expanded="False" title="Constructing consensus tree">
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446 <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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447 <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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448 <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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449 <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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450 <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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451 <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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452 </section>
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453 <section name="computing_robinson_foulds" expanded="False" title="Computing Robinson-Foulds distance">
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454 <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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455 <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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456 <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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457 </section>
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458 <section name="generating_random" expanded="False" title="Generating random trees">
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459 <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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460 <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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461 <param argument="-rcat" type="boolean" truevalue="-rcat" falsevalue="" checked="false" label="Like -r, but a random caterpillar tree is created."/>
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462 <param argument="-rbal" type="boolean" truevalue="-rbal" falsevalue="" checked="false" label="Like -r, but a random balanced tree is created."/>
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463 <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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464 <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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465 <sanitizer>
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466 <valid initial="string.digits,string.whitespace" />
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467 </sanitizer>
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468 </param>
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469 </section>
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470 </section>
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471 <section name="bootstrap_parameters" title="Bootstrap Parameters">
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472 <section name="ultrafast_bootstrap" expanded="False" title="Ultrafast bootstrap parameters">
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473 <param argument="-bb" type="integer" optional="true" label="Specify number of bootstrap replicates (&gt;=1000)."/>
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474 <param argument="-wbt" type="boolean" truevalue="-wbt" falsevalue="" checked="false" label="Turn on writing bootstrap trees to .ufboot file"/>
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475 <param argument="-wbtl" type="boolean" truevalue="-wbtl" falsevalue="" checked="false" label="Like -wbt but bootstrap trees written with branch lengths"/>
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476 <param argument="-nm" type="integer" value="1000" optional="true" label="Specify maximum number of iterations to stop"/>
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477 <param argument="-bcor" type="float" value="0.99" optional="true" label="Specify minimum correlation coefficient for UFBoot convergence criterion"/>
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478 <param argument="-nstep" type="integer" value="100" optional="true" label="Specify iteration interval checking for UFBoot convergence"/>
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479 <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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480 <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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481 <sanitizer>
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482 <valid initial="string.ascii_uppercase" />
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483 </sanitizer>
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484 </param>
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485 <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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486 </section>
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487 <section name="nonparametric_bootstrap" expanded="False" title="Nonparametric bootstrap">
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488 <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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489 <param argument="-bc" type="boolean" truevalue="-bc" falsevalue="" checked="false" label="Like -b but omit analysis on original alignment."/>
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490 <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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491 </section>
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492 </section>
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493 <section name="miscellaneous_options" expanded="False" title="Miscellaneous options">
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494 <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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495 <expand macro="sanitize_query"
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496 validinitial="string.digits,string.punctuation" />
1
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497 </param>
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498 </section>
0
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499 </inputs>
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500 <outputs>
1
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501 <data name='bionj' format='nhx' from_work_dir="*.bionj" label="${tool.name} on ${on_string}: BIONJ Tree" />
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502 <data name='treefile' format='nhx' from_work_dir="*.treefile" label="${tool.name} on ${on_string}: MaxLikelihood Tree" />
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503 <data name='contree' format='nhx' from_work_dir="*.contree" label="${tool.name} on ${on_string}: Consensus Tree" />
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504 <data name='mldist' format='mldist' from_work_dir="*.mldist" label="${tool.name} on ${on_string}: MaxLikelihood Distance Matrix"/>
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505 <data name='splits.nex' format='nex' from_work_dir="*.splits.nex" label="${tool.name} on ${on_string}: Occurence Frequencies in Bootstrap Trees" />
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506 <data name='iqtree' format='iqtree' from_work_dir="*.iqtree" label="${tool.name} on ${on_string}: Report and Final Tree" />
0
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507 </outputs>
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508 <tests>
1
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509 <test>
0
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510 <param name="seed" value="1257" />
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511 <param name="st" value="AA" />
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512 <param name="s" value="example.phy" />
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513 <param name="m" value="TESTNEW" />
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514 <param name="msub" value="nuclear" />
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515 <param name="madd" value="LG4M,LG4X" />
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516 <param name="merit" value="AICc" />
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
517 <param name="bb" value="1000" />
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
518 <output name='bionj'>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
519 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
520 <has_text_matching expression=".*Human.*Whale.*" />
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
521 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
522 </output>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
523 <output name='iqtree'>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
524 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
525 <has_text_matching expression="VT\+F\+R3(\s+((-|\d|\.)+))+" />
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
526 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
527 </output>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
528 <output name='mldist'>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
529 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
530 <has_line_matching expression="^Frog(\s+((\d|\.)+))+\s+$" />
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
531 <has_line_matching expression="^Whale(\s+((\d|\.)+))+\s+$" />
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
532 <has_line_matching expression="^Cow(\s+((\d|\.)+))+\s+$" />
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
533 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
534 </output>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
535 <output name='treefile'>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
536 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
537 <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
538 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
539 </output>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
540 <output name='contree' >
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
541 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
542 <has_line_matching
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
543 expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*\)\d+:(\d|\.)+,.*" />
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
544 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
545 </output>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
546 <output name='splits.nex'>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
547 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
548 <has_line line="BEGIN Splits;" />
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
549 <has_line line="END; [Splits]" />
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
550 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
551 </output>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
552 </test>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
553 <test>
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
554 <!-- bootstrap sans model -->
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
555 <param name="seed" value="1257" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
556 <param name="st" value="AA" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
557 <param name="s" value="example.phy" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
558 <!-- <param name="m" value="TESTONLY" /> -->
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
559 <param name="msub" value="nuclear" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
560 <param name="cmin" value="2" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
561 <param name="cmax" value="10" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
562 <param name="merit" value="AICc" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
563 <param name="madd" value="LG4M,LG4X" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
564 <param name="ninit" value="100" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
565 <param name="ntop" value="20" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
566 <param name="nbest" value="5" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
567 <param name="nstop" value="100" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
568 <param name="sprrad" value="6" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
569 <param name="pers" value="0.5" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
570 <param name="minsup" value="0.0" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
571 <param name="nm" value="1000" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
572 <param name="bcor" value="0.99" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
573 <param name="nstep" value="100" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
574 <param name="beps" value="0.5" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
575 <param name="b" value="2" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
576 <output name='iqtree'>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
577 <assert_contents>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
578 <has_text_matching expression="VT\+F\+I(\s+((-|\d|\.)+))+" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
579 </assert_contents>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
580 </output>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
581 <output name='treefile'>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
582 <assert_contents>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
583 <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
584 </assert_contents>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
585 </output>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
586 </test>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
587 <test>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
588 <!-- model sans bootstrap -->
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
589 <param name="seed" value="1257" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
590 <param name="st" value="AA" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
591 <param name="s" value="example.phy" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
592 <param name="m" value="TESTONLY" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
593 <param name="msub" value="nuclear" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
594 <param name="cmin" value="2" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
595 <param name="cmax" value="10" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
596 <param name="merit" value="AICc" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
597 <param name="madd" value="LG4M,LG4X" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
598 <param name="ninit" value="100" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
599 <param name="ntop" value="20" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
600 <param name="nbest" value="5" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
601 <param name="nstop" value="100" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
602 <param name="sprrad" value="6" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
603 <param name="pers" value="0.5" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
604 <param name="minsup" value="0.0" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
605 <param name="nm" value="1000" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
606 <param name="bcor" value="0.99" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
607 <param name="nstep" value="100" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
608 <param name="beps" value="0.5" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
609 <!-- <param name="b" value="100" /> -->
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
610 <output name='iqtree'>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
611 <assert_contents>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
612 <has_text_matching expression="VT\+F\+I(\s+((-|\d|\.)+))+" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
613 </assert_contents>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
614 </output>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
615 <output name='treefile'>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
616 <assert_contents>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
617 <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
618 </assert_contents>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
619 </output>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
620 </test>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
621 <test>
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
622 <param name='s' value='example.phy' />
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
623 <output name='iqtree'>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
624 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
625 <has_text_matching expression=".*Human.*Whale.*" />
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
626 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
627 </output>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
628 <output name='treefile'>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
629 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
630 <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
631 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
632 </output>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
633 </test>
3
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
634 <test>
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
635 <param name='s' value='example.phy' />
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
636 <param name='opt_custommodel' value='true' />
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
637 <param name='m' value='GTR+G{0.9}' />
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
638 <output name='iqtree'>
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
639 <assert_contents>
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
640 <has_text_matching expression=".*Human.*Whale.*" />
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
641 </assert_contents>
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
642 </output>
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
643 <output name='treefile'>
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
644 <assert_contents>
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
645 <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
646 </assert_contents>
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
647 </output>
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
648 </test>
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
649 </tests>
2
d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
650 <help><![CDATA[
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
651 IQ-TREE
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
652 =======
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
653
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
654 The full documentation can be found here_.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
655
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
656 .. _here : http://www.iqtree.org/doc/
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
657
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
658 General Tutorial
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
659 ===================
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
660
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
661 Input data
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
662 ----------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
663
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
664 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:
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
665
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
666 .. _PHYLIP: http://evolution.genetics.washington.edu/phylip/doc/sequence.html
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
667
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
668 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
669
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
670 7 28
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
671 Frog AAATTTGGTCCTGTGATTCAGCAGTGAT
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
672 Turtle CTTCCACACCCCAGGACTCAGCAGTGAT
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
673 Bird CTACCACACCCCAGGACTCAGCAGTAAT
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
674 Human CTACCACACCCCAGGAAACAGCAGTGAT
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
675 Cow CTACCACACCCCAGGAAACAGCAGTGAC
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
676 Whale CTACCACGCCCCAGGACACAGCAGTGAT
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
677 Mouse CTACCACACCCCAGGACTCAGCAGTGAT
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
678
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
679 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:
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
680
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
681 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
682
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
683 >Frog
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
684 AAATTTGGTCCTGTGATTCAGCAGTGAT
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
685 >Turtle
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
686 CTTCCACACCCCAGGACTCAGCAGTGAT
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
687 >Bird
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
688 CTACCACACCCCAGGACTCAGCAGTAAT
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
689 >Human
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
690 CTACCACACCCCAGGAAACAGCAGTGAT
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
691 >Cow
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
692 CTACCACACCCCAGGAAACAGCAGTGAC
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
693 >Whale
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
694 CTACCACGCCCCAGGACACAGCAGTGAT
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
695 >Mouse
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
696 CTACCACACCCCAGGACTCAGCAGTGAT
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
697
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
698 **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.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
699
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
700 .. _MAFFT: http://mafft.cbrc.jp/alignment/software/
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
701 .. _ClustalW: http://www.clustal.org
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
702
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
703
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
704 Running example
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
705 ---------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
706
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
707 From the download_ there is an example alignment called `example.phy`
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
708 in PHYLIP format. This example contains parts of the mitochondrial DNA sequences of several animals (Source: `Phylogenetic Handbook`_)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
709
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
710 .. _`Phylogenetic Handbook` : http://www.kuleuven.be/aidslab/phylogenybook/home.html)).
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
711 .. _download: http://www.iqtree.org/#download
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
712
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
713 You can now start to reconstruct a maximum-likelihood tree
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
714 from this alignment by entering (assuming that you are now in the same folder with `example.phy`):
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
715
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
716 ::iqtree -s example.phy -st AA -seed 9999 -m TESTNEW -msub nuclear -madd LG4M,LG4x -merit AICc -bb 2000
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
717
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
718 * **-s** is the option to specify the name of the alignment file
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
719
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
720 * **-st** specifies the sequence type as amino-acid
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
721
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
722 * **-seed** ensures that the output files remain the same for subsequent runs
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
723
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
724 * **-m** sets the modelling parameter for standard model selection
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
725
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
726 * **-msub** determines the type sub-modelling
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
727
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
728 * **-madd** provides an additional selection mixed models
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
729
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
730 * **-merit** asserts the type of optimality criterion
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
731
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
732 * **-bb** defines the number of replicates
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
733
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
734
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
735 Each of these parameters are available under the relevant sub-sections in the main tool interface.
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
736
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
737 At the end of the run IQ-TREE will write several output files including:
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
738
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
739 * **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).
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
740
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
741 * **example.phy.treefile**: the ML tree in NEWICK format, which can be visualized by any supported tree viewer programs like FigTree or iTOL.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
742
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
743 **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.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
744
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
745 For this example data the resulting maximum-likelihood tree may look like this (extracted from **.iqtree** file):
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
746
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
747 **NOTE**: Tree is UNROOTED although outgroup taxon 'LngfishAu' is drawn at root
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
748
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
749 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
750
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
751 +--------------LngfishAu
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
752 |
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
753 | +--------------LngfishSA
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
754 +--------|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
755 | +--------------LngfishAf
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
756 |
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
757 | +-------------------Frog
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
758 +------|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
759 | +-----------------Turtle
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
760 | +-----|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
761 | | | +-----------------------Sphenodon
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
762 | | | +--|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
763 | | | | +--------------------------Lizard
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
764 | | +---|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
765 | | | +---------------------Crocodile
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
766 | | +------|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
767 | | +------------------Bird
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
768 +---------|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
769 | +----------------Human
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
770 | +--|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
771 | | | +--------Seal
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
772 | | +--|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
773 | | | +-------Cow
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
774 | | +---|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
775 | | +---------Whale
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
776 | +----|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
777 | | | +------Mouse
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
778 | | +---------|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
779 | | +--------Rat
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
780 +----------|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
781 | +----------------Platypus
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
782 +---|
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
783 +-------------Opossum
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
784
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
785
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
786 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.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
787
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
788 Choosing the right substitution model
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
789 -------------------------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
790
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
791 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.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
792
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
793 .. _Models: http://www.iqtree.org/doc/Substitution-Models#binary-and-morphological-models
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
794
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
795
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
796 ------------------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
797
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
798 Advanced Parameter Selection
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
799 ============================
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
800
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
801 Using codon models
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
802 ------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
803
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
804 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):
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
805
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
806 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
807
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
808 iqtree -s coding_gene.phy -st CODON
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
809
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
810 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.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
811
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
812 Note that the above command assumes the standard genetic code. If your sequences follow 'The Invertebrate Mitochondrial Code', then run:
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
813
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
814 ::
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
815
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
816 iqtree -s coding_gene.phy -st CODON5
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
817
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
818 Note that ModelFinder works for codon alignments. IQ-TREE version >= 1.5.4 will automatically invokes ModelFinder to find the best-fit codon model.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
819
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
820
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
821 Assessing branch supports with ultrafast bootstrap approximation
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
822 ----------------------------------------------------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
823
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
824 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:
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
825
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
826 B.Q. Minh, M.A.T. Nguyen, and A. von Haeseler (2013) Ultrafast approximation for phylogenetic bootstrap. _Mol. Biol. Evol., 30:1188-1195.
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
827
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
828 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
829
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
830 iqtree -s example.phy -m TIM2+I+G -bb 1000
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
831
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
832 **-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:
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
833
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
834 * **example.phy.contree**: the consensus tree with assigned branch supports where branch lengths are optimized on the original alignment.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
835
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
836 * **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.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
837
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
838 * **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.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
839
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
840 .. _SplitsTree: http://www.splitstree.org
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
841
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
842
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
843 Reducing impact of severe model violations with UFBoot
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
844 ------------------------------------------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
845
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
846 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.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
847
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
848 Thus, if severe model violations are present in the data set at hand, users are advised to append **-bnni** to the regular UFBoot command:
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
849
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
850 iqtree -s example.phy -m TIM2+I+G -bb 1000 -bnni
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
851
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
852 For more details see:
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
853
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
854 D.T. Hoang, O. Chernomor, A. von Haeseler, B.Q. Minh, L.S. Vinh (2017) UFBoot2: Improving the ultrafast bootstrap approximation.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
855
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
856
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
857 Assessing branch supports with standard nonparametric bootstrap
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
858 ----------------------------------------------------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
859
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
860 The standard nonparametric bootstrap is invoked by the **-b** option:
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
861
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
862 iqtree -s example.phy -m TIM2+I+G -b 100
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
863
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
864 **-b** specifies the number of bootstrap replicates where 100
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
865 is the minimum recommended number. The output files are similar to those produced by the UFBoot procedure.
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
866
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
867
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
868
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
869 Assessing branch supports with single branch tests
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
870 --------------------------------------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
871
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
872 IQ-TREE provides an implementation of the SH-like approximate likelihood ratio test ([Guindon et al., 2010]). To perform this test, run:
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
873
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
874 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
875
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
876 iqtree -s example.phy -m TIM2+I+G -alrt 1000
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
877
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
878 **-alrt** specifies the number of bootstrap replicates for SH-aLRT where 1000 is the minimum number recommended.
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
879
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
880 IQ-TREE also supports other tests such as the aBayes test (Anisimova et al., 2011) and the local bootstrap test (Adachi and Hasegawa, 1996).
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
881
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
882 You can also perform both SH-aLRT and the ultrafast bootstrap within one single run:
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
883
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
884 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
885
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
886 iqtree -s example.phy -m TIM2+I+G -alrt 1000 -bb 1000
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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887
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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888 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:
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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889
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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890 **NOTE**: Tree is UNROOTED although outgroup taxon 'LngfishAu' is drawn at root
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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891 Numbers in parentheses are SH-aLRT support (%) / ultrafast bootstrap support (%)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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892
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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893 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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894
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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895 +-------------LngfishAu
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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896 |
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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897 | +--------------LngfishSA
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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898 +-------| (100/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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899 | +------------LngfishAf
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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900 |
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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901 | +--------------------Frog
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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902 +------| (99.8/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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903 | +-----------------Turtle
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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904 | +--| (85/72)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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905 | | | +------------------------Crocodile
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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906 | | +----| (96.5/97)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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907 | | +------------------Bird
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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908 | +--| (39/51)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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909 | | +---------------------------Sphenodon
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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910 | +-----| (98.2/99)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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911 | | +-------------------------------Lizard
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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912 +---------| (100/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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913 | +--------------Human
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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914 | +--| (92.3/93)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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915 | | | +------Seal
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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916 | | +--| (68.3/75)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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917 | | | +-----Cow
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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918 | | +--| (99.7/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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919 | | +-------Whale
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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920 | +----| (99.1/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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921 | | | +---Mouse
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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922 | | +---------| (100/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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923 | | +------Rat
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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924 +-----------| (100/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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925 | +--------------Platypus
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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926 +--| (93/98)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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927 +-----------Opossum
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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928
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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929
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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930 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.
2
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931 ]]></help>
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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932 <citations>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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933 <citation type="doi">10.1093/molbev/msu300</citation>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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934 <citation type="doi">10.1093/molbev/mst024</citation>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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935 </citations>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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936 </tool>