Mercurial > repos > iuc > iqtree

annotate iqtree.xml @ 13:24d024316465 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 25f53344278285ac5e75ac902aec60a38921aa12
author iuc
date Tue, 09 Apr 2024 05:10:40 +0000
parents 9b892d7f82cc
children 70acec670c30
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9b892d7f82cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3b1c44e42b042ccbbe2d9e01c77d18f109d4984f"
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1 <tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
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2 <description>Phylogenomic / evolutionary tree construction from multiple sequences</description>
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3 <macros>
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4 <import>iqtree_macros.xml</import>
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5 </macros>
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24d024316465 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 25f53344278285ac5e75ac902aec60a38921aa12
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6 <expand macro="xrefs"/>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 iqtree
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10 --prefix PREF
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11 #if $general_options.short_alignments:
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12 -T 1
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13 #else:
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14 -T \${GALAXY_SLOTS:-10}
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15 #end if
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16 --redo
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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 $general_options.s
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20 -s '$general_options.s'
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21 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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22
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23 #if $general_options.o
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24 -o '$general_options.o'
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25 #end if
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26 --seqtype $general_options.seqtype
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27 ## file
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28 #if $general_options.t
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29 -t '$general_options.t'
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30 $tree_parameters.constructing_consensus.contree
563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
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31 $tree_parameters.constructing_consensus.connet
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32 #if str($tree_parameters.constructing_consensus.burnin) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
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33 --burnin '$tree_parameters.constructing_consensus.burnin'
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34 #end if
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36 ## file
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37 #if $tree_parameters.constructing_consensus.support
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38 --support '$tree_parameters.constructing_consensus.support'
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39 #end if
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288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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41 #if str($tree_parameters.constructing_consensus.suptag) != ''
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42 --suptag '$tree_parameters.constructing_consensus.suptag'
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43 #end if
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45 ## file
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46 #if $tree_parameters.computing_robinson_foulds.tree_dist_all
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47 $tree_parameters.computing_robinson_foulds.tree_dist_all
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48 --tree-dist $tree_parameters.computing_robinson_foulds.tree_dist
563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
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49 --tree-dist2 $tree_parameters.computing_robinson_foulds.tree_dist2
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50 #end if
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51 $tree_parameters.ancestral_state.ancestral
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52 #if $tree_parameters.ancestral_state.asr_min:
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
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53 --asr-min $tree_parameters.ancestral_state.asr_min
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
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54 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
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55 #if $tree_parameters.concordance_factor.gcf:
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
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56 --gcf '$tree_parameters.concordance_factor.gcf'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
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57 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
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58 #if $tree_parameters.concordance_factor.scf:
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
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59 --scf '$tree_parameters.concordance_factor.scf'
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60 #end if
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61 $tree_parameters.concordance_factor.df_tree
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62 $tree_parameters.concordance_factor.cf_verbose
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63 $tree_parameters.concordance_factor.cf_quartet
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64 $tree_parameters.symmetry_test.symtest
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65 $tree_parameters.symmetry_test.symtest_remove_bad
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66 $tree_parameters.symmetry_test.symtest_remove_good
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67 $tree_parameters.symmetry_test.symtest_keep_zero
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68 #if $tree_parameters.symmetry_test.symtest_pval:
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69 --symtest-pval $tree_parameters.symmetry_test.symtest_pval
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70 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
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71 #if $tree_parameters.symmetry_test.symtest_type:
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72 --symtest-type $tree_parameters.symmetry_test.symtest_type
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73 #end if
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74 #end if
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75
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76 ## date options
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77 #if str($time_tree.date_source.select_source) == 'dataset':
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78 #if $time_tree.date_source.date:
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79 --date '$time_tree.date_source.date'
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80 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
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81 #elif str($time_tree.date_source.select_source) == 'input':
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82 --date TAXNAME
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83 #if str($time_tree.date_source.date_tip) != '':
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84 --date-tip '$time_tree.date_source.date_tip'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
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85 #end if
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86 #if str($time_tree.date_source.date_root) != '':
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87 --date-root '$time_tree.date_source.date_root'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
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88 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
89 #if str($time_tree.date_source.date_ci) != '':
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
90 --date-ci '$time_tree.date_source.date_ci'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
91 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
92 #if str($time_tree.date_source.clock_sd) != '':
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
93 --clock-sd '$time_tree.date_source.clock_sd'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
94 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
95 #if str($time_tree.date_source.date_outlier) != '':
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
96 --date-outlier '$time_tree.date_source.date_outlier'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
97 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
98 #if str($time_tree.date_source.date_options) != '':
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
99 --date-options '$time_tree.date_source.date_options'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
100 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
101 --dating LSD
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
102 $time_tree.date_source.date_no_outgroup
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
103 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
104
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
105 ## file
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
106 #if str($general_options.epsilon) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
107 --epsilon '$general_options.epsilon'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
108 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
109
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
110 #if str($general_options.seed) != ''
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
111 --seed '$general_options.seed'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
112 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
113
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
114 $general_options.keep_ident
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
115 $general_options.safe
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
116
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
117 #if str($likelihood_mapping.lmap) != ''
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
118 --lmap '$likelihood_mapping.lmap'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
119 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
120
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
121 ## file
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
122 #if $likelihood_mapping.lmclust
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
123 --lmclust '$likelihood_mapping.lmclust'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
124 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
125
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
126 $likelihood_mapping.quartetlh
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
127
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
128 #if $modelling_parameters.automatic_model.cond_model.opt_custommodel:
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
129 -m '$modelling_parameters.automatic_model.cond_model.m'
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
130 #else:
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
131 #if str($modelling_parameters.automatic_model.cond_model.m) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
132 #if $modelling_parameters.automatic_model.cond_model.additional_models:
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
133 -m '$modelling_parameters.automatic_model.cond_model.m${$modelling_parameters.automatic_model.cond_model.additional_models}'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
134 #else:
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
135 -m '$modelling_parameters.automatic_model.cond_model.m'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
136 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
137 #end if
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
138 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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139
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
140 #if str($modelling_parameters.automatic_model.merge_strategy.merge) != 'none':
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
141 --merge $modelling_parameters.automatic_model.merge_strategy.merge
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
142 #if str($modelling_parameters.automatic_model.merge_strategy.merge) == 'rcluster':
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
143 --rcluster $modelling_parameters.automatic_model.merge_strategy.rcluster
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
144 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
145 #if str($modelling_parameters.automatic_model.merge_strategy.merge) == 'rclusterf':
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
146 --rclusterf $modelling_parameters.automatic_model.merge_strategy.rclusterf
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
147 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
148 #if str($modelling_parameters.automatic_model.merge_strategy.merge) in ['rcluster', 'rclusterf']:
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
149 --rcluster-max $modelling_parameters.automatic_model.merge_strategy.rcluster_max
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
150 #end if
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
151 #end if
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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parents: 0
diff changeset
152
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
153 #if str($modelling_parameters.automatic_model.mset) != ''
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
154 --mset '$modelling_parameters.automatic_model.mset'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
155 #end if
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
156
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
157 #if str($modelling_parameters.automatic_model.msub) != ''
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
158 --msub '$modelling_parameters.automatic_model.msub'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
159 #end if
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
160
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
161 #if str($modelling_parameters.automatic_model.mfreq) != ''
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
162 --mfreq '$modelling_parameters.automatic_model.mfreq'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
163 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
164
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
165 #if str($modelling_parameters.automatic_model.mrate) != ''
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
166 --mrate '$modelling_parameters.automatic_model.mrate'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
167 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
168
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
169 #if str($modelling_parameters.automatic_model.cmin) != ''
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
170 --cmin '$modelling_parameters.automatic_model.cmin'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
171 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
172
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
173 #if str($modelling_parameters.automatic_model.cmax) != ''
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
174 --cmax '$modelling_parameters.automatic_model.cmax'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
175 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
176
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
177 #if str($modelling_parameters.automatic_model.merit) != ''
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
178 --merit '$modelling_parameters.automatic_model.merit'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
179 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
180
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
181 $modelling_parameters.automatic_model.mtree
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
182
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
183 #if str($modelling_parameters.automatic_model.madd) != ''
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
184 --madd '$modelling_parameters.automatic_model.madd'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
185 #end if
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 $modelling_parameters.automatic_model.mdef
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
189 --mdef '$modelling_parameters.automatic_model.mdef'
0
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:
diff changeset
191
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
192 $modelling_parameters.automatic_model.modelomatic
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
193 $modelling_parameters.specifying_substitution.mix_opt
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
194
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
195 #if str($modelling_parameters.rate_heterogeneity.alpha_min) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
196 --alpha-min '$modelling_parameters.rate_heterogeneity.alpha_min'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
197 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
198
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
199 $modelling_parameters.rate_heterogeneity.gamma_median
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
200
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
201 #if str($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
202 -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
203 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
204
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
205 $modelling_parameters.rate_heterogeneity.opt_gamma_inv
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
206 $modelling_parameters.rate_heterogeneity.rate
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
207
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
208 #if str($modelling_parameters.partition_model.model_selection.model) != 'none':
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
209 -$modelling_parameters.partition_model.model_selection.model '$modelling_parameters.partition_model.model_selection.model_file'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
210 #if str($modelling_parameters.partition_model.model_selection.subsample) != '':
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
211 --subsample $modelling_parameters.partition_model.model_selection.subsample
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
212 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
213 #if str($modelling_parameters.partition_model.model_selection.subsample_seed) != '':
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
214 --subsample-seed $modelling_parameters.partition_model.model_selection.subsample_seed
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
215 #end if
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
216 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
217
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
218 ## file
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
219 #if $modelling_parameters.site_specific_frequency.tree_freq
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
220 --tree-freq '$modelling_parameters.site_specific_frequency.tree_freq'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
221 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
222
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
223 #if str($modelling_parameters.site_specific_frequency.site_freq) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
224 --site-freq '$modelling_parameters.site_specific_frequency.site_freq'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
225 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
226
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
227 $modelling_parameters.site_specific_frequency.freq_max
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
228
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
229 #if str($tree_parameters.tree_search.ninit) != ''
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
230 --ninit '$tree_parameters.tree_search.ninit'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
231 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
232
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
233 #if str($tree_parameters.tree_search.ntop) != ''
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
234 --ntop '$tree_parameters.tree_search.ntop'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
235 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
236
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
237 #if str($tree_parameters.tree_search.nbest) != ''
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
238 --nbest '$tree_parameters.tree_search.nbest'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
239 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
240
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
241 #if str($tree_parameters.tree_search.nstop) != ''
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
242 --nstop '$tree_parameters.tree_search.nstop'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
243 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
244
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
245 #if str($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
246 -n '$tree_parameters.tree_search.n'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
247 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
248
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
249 #if str($tree_parameters.tree_search.radius) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
250 --radius '$tree_parameters.tree_search.radius'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
251 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
252
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
253 #if str($tree_parameters.tree_search.perturb) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
254 --perturb '$tree_parameters.tree_search.perturb'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
255 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
256
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
257 $tree_parameters.tree_search.allnni
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
258 $tree_parameters.tree_search.tree_fix
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
259 $tree_parameters.tree_search.fast
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
260 $tree_parameters.tree_search.polytomy
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
261 $tree_parameters.tree_search.treels
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
262 $tree_parameters.tree_search.show_lh
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
263 $tree_parameters.tree_search.terrace
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
264
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
265 ## file
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
266 #if $tree_parameters.tree_search.g
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
267 -g '$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
268 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
269
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
270 #if str($tree_parameters.single_branch.alrt) != ''
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
271 --alrt '$tree_parameters.single_branch.alrt'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
272 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
273
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
274 $tree_parameters.single_branch.abayes
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
275
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
276 #if str($tree_parameters.single_branch.lbp) != ''
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
277 --lbp '$tree_parameters.single_branch.lbp'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
278 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
279
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
280 ## file
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
281 #if $tree_parameters.tree_topology.trees
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
282 --trees '$tree_parameters.tree_topology.trees'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
283 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
284
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
285 #if str($tree_parameters.tree_topology.test) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
286 --test '$tree_parameters.tree_topology.test'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
287 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
288
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
289 $tree_parameters.tree_topology.test_weight
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
290 $tree_parameters.tree_topology.test_au
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
291
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
292 #if str($tree_parameters.constructing_consensus.sup_min) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
293 --sup-min '$tree_parameters.constructing_consensus.sup_min'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
294 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
295
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
296
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
297 #if str($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
298 -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:
diff changeset
299 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
300
6
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
301 #if $tree_parameters.generating_random.rand
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
302 $tree_parameters.generating_random.rand
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
303 #end if
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
304
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
305 #if str($tree_parameters.generating_random.branch_min) != '' and str($tree_parameters.generating_random.branch_mean) != '' and str($tree_parameters.generating_random.branch_max) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
306 --rlen $tree_parameters.generating_random.branch_min $tree_parameters.generating_random.branch_mean $tree_parameters.generating_random.branch_max
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
307 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
308
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
309 #if str($bootstrap_parameters.ultrafast_bootstrap.ufboot) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
310 --ufboot '$bootstrap_parameters.ultrafast_bootstrap.ufboot'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
311 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
312
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
313 #if str($bootstrap_parameters.ultrafast_bootstrap.ufjack) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
314 --ufjack '$bootstrap_parameters.ultrafast_bootstrap.ufjack'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
315 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
316
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
317 #if str($bootstrap_parameters.ultrafast_bootstrap.jack_prop) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
318 --jack-prop '$bootstrap_parameters.ultrafast_bootstrap.jack_prop'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
319 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
320
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
321 #if str($bootstrap_parameters.ultrafast_bootstrap.sampling) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
322 --sampling '$bootstrap_parameters.ultrafast_bootstrap.sampling'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
323 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
324
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
325 $bootstrap_parameters.ultrafast_bootstrap.boot_trees
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
326 $bootstrap_parameters.ultrafast_bootstrap.wbtl
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
327
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
328 #if str($bootstrap_parameters.ultrafast_bootstrap.nmax) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
329 --nmax '$bootstrap_parameters.ultrafast_bootstrap.nmax'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
330 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
331
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
332 #if str($bootstrap_parameters.ultrafast_bootstrap.nstep) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
333 --nstep '$bootstrap_parameters.ultrafast_bootstrap.nstep'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
334 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
335
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
336 #if str($bootstrap_parameters.ultrafast_bootstrap.bcor) != ''
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
337 --bcor '$bootstrap_parameters.ultrafast_bootstrap.bcor'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
338 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
339
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
340 #if str($bootstrap_parameters.ultrafast_bootstrap.beps) != ''
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
341 --beps '$bootstrap_parameters.ultrafast_bootstrap.beps'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
342 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
343
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
344 $bootstrap_parameters.ultrafast_bootstrap.bnni
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
345
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
346 #if str($bootstrap_parameters.nonparametric_bootstrap.boot) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
347 --boot '$bootstrap_parameters.nonparametric_bootstrap.boot'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
348 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
349
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
350 #if str($bootstrap_parameters.nonparametric_bootstrap.jack) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
351 --jack '$bootstrap_parameters.nonparametric_bootstrap.jack'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
352 #end if
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
353
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
354 #if str($bootstrap_parameters.nonparametric_bootstrap.jack_prop) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
355 --jack-prop '$bootstrap_parameters.nonparametric_bootstrap.jack_prop'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
356 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
357
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
358 $bootstrap_parameters.nonparametric_bootstrap.bcon
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
359 $bootstrap_parameters.nonparametric_bootstrap.bonly
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
360 $bootstrap_parameters.nonparametric_bootstrap.tbe
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
361
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
362 #if str($miscellaneous_options.fconst) != ''
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
363 --fconst '$miscellaneous_options.fconst'
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
364 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
365 ]]>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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366 </command>
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367 <inputs>
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368 <section name="general_options" expanded="true" title="General options">
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369 <param argument="-s" type="data" format="txt,fasta,phylip,nex,clustal,msf" optional="true" label="Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format."/>
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370 <param argument="-o" type="text" optional="true" label="Comma-separated list of taxons to output">
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371 <expand macro="sanitize_query" />
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372 </param>
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373
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374 <param type="boolean" name="short_alignments" label="Short alignments" help="IQ-TREE will fail if given too many threads on input data that consists of short alignments, this option will force the use of a single thread." />
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375 <param argument="--seqtype" 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">
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376 <help><![CDATA[
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377 Note that --seqtype 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.
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378 <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 --seqtype NT2AA5 for the Invertebrate Mitochondrial Code (see genetic code table).]]>
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379 </help>
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380 <option value="DNA">DNA</option>
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381 <option value="AA">AA</option>
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382 <option value="BIN">BIN</option>
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383 <option value="MORPH">MORPH</option>
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384 <option value="CODON">CODON</option>
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385 <option value="NT2AA">NT2AA</option>
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386 </param>
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387 <param argument="-t" type="data" format="nhx" optional="true" label="Specify a file containing starting tree for tree search"/>
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388 <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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389 <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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390 <param argument="--epsilon" type="float" optional="true" min="0" max="1" label="Likelihood epsilon for parameter estimate" />
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391 <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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392 </section>
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393 <section name="time_tree" expanded="false" title="Time Tree Reconstruction">
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394 <conditional name="date_source">
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395 <param name="select_source" type="select" label="Source of date information">
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396 <option value="none">Skip time tree reconstruction</option>
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397 <option value="dataset">Text file</option>
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398 <option value="input">Derive from input</option>
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399 </param>
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400 <when value="none" />
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401 <when value="input" />
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402 <when value="dataset">
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403 <param argument="--date" type="data" format="txt,tabular" optional="true" label="File containing dates of tips or ancestral nodes" />
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404 </when>
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405 </conditional>
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406 <param argument="--date-tip" type="text" optional="true" label="Tip dates as a real number or YYYY-MM-DD">
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407 <expand macro="sanitize_query" />
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408 </param>
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409 <param argument="--date-root" type="text" optional="true" label="Root date as a real number or YYYY-MM-DD">
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410 <expand macro="sanitize_query" />
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411 </param>
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412 <param argument="--date-ci" type="integer" optional="true" label="Number of replicates to compute confidence interval" />
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413 <param argument="--clock-sd" type="float" optional="true" label="Standard-deviation for lognormal relaxed clock" />
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414 <param argument="--date-no-outgroup" type="boolean" truevalue="--date-no-outgroup" falsevalue="" label="Exclude outgroup from time tree" />
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415 <param argument="--date-outlier" type="integer" optional="true" label="Z-score cutoff to remove outlier tips/nodes" />
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416 <param argument="--date-options" type="text" optional="true" label="Extra options passing directly to LSD2">
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417 <expand macro="sanitize_query" />
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418 </param>
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419 </section>
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420 <section name="likelihood_mapping" expanded="False" title="Likelihood mapping analysis">
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421 <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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422 <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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423 <param argument="--quartetlh" type="boolean" truevalue="--quartetlh" falsevalue="" checked="false" label="Write quartet log-likelihoods into .lmap.quartetlh file (typically not needed)."/>
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424 </section>
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425 <section name="modelling_parameters" title="Modelling Parameters">
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426 <section name="automatic_model" expanded="False" title="Automatic model selection">
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427 <conditional name="cond_model" >
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428
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429 <param name="opt_custommodel" type="select" label="Do you want to use a custom model" help="See http://www.iqtree.org/doc/Substitution-Models">
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430 <option value="true" selected="True">Yes, I want to use a custom model</option>
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431 <option value="false">No, a custom model is not needed</option>
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432 </param>
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433 <when value="true">
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434 <param argument="-m" type="text" label="Model">
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435 <expand macro="sanitize_query"
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436 validinitial="string.ascii_uppercase,string.digits,string.punctuation" />
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437 </param>
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438 </when>
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439 <when value="false">
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440 <param argument="-m" type="select" label="Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein)" >
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441 <help><![CDATA[
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442 <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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443 IQ-TREE also works for codon, binary and morphological data.
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444 <table>
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445 <tr>
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446 <td><i>TESTONLY</i></td>
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447 <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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448 </tr>
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449 <tr>
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450 <td><i>TEST</i></td>
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451 <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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452 </tr>
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453 <tr>
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454 <td><i>MF</i></td>
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455 <td>Best-fit model selection without tree reconstruction.</td>
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456 </tr>
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457 <tr>
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458 <td><i>MFP</i></td>
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459 <td>Extended model selection with FreeRate heterogeneity immediately followed by tree inference.</td>
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460 </tr>
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461 </table>
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462 ]]>
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463 </help>
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464 <option value="" selected="true">(None)</option>
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465 <option value="TESTONLY">Standard model selection</option>
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466 <option value="TEST">Standard model selection followed by tree inference</option>
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467 <option value="MF">Extended model selection with FreeRate heterogeneity</option>
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468 <option value="MFP">Extended model selection followed by tree inference</option>
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469 </param>
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470 <param name="additional_models" type="text" optional="true" label="Additional model specifications" help="See http://www.iqtree.org/doc/Substitution-Models">
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471 <expand macro="sanitize_query" />
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472 </param>
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473 </when>
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474 </conditional>
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475 <conditional name="merge_strategy">
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476 <param argument="--merge" type="select" label="Merge partitions">
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477 <option value="none">Do not merge</option>
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478 <option value="rclusterf">Merge using rcluster relaxed algorithm</option>
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479 <option value="rcluster">Merge using rcluster algorithm</option>
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480 <option value="greedy">Merge using greedy algorithm</option>
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481 </param>
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482 <when value="none" />
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483 <when value="greedy" />
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484 <when value="rcluster">
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485 <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, giving the value 10 only the top 10% partition schemes are considered to save computations." />
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486 <param argument="--rcluster-max" type="integer" optional="true" label="Max number of partition pairs" />
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487 </when>
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488 <when value="rclusterf">
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489 <param argument="--rclusterf" 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, giving the value 10 only the top 10% partition schemes are considered to save computations." />
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490 <param argument="--rcluster-max" type="integer" optional="true" label="Max number of partition pairs" />
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491 </when>
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492 </conditional>
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493 <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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494 <expand macro="sanitize_query"
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495 validinitial="string.ascii_letters,string.punctuation" />
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496 </param>
5
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497 <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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498 <option value="nuclear">nuclear</option>
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499 <option value="mitochondrial">mitochondrial</option>
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500 <option value="chloroplast">chloroplast</option>
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501 <option value="viral">viral</option>
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502 </param>
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503 <param argument="--mfreq" type="text" optional="true" label="Specify a comma-separated list of frequency types for model selection" >
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504 <expand macro="sanitize_query"
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505 validinitial="string.ascii_uppercase,string.digits,x,string.punctuation" />
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506 </param>
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507 <param argument="--mrate" type="text" optional="true" label="Specify a comma-separated list of rate heterogeneity types for model selection">
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508 <expand macro="sanitize_query"
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509 validinitial="string.ascii_uppercase,string.punctuation" />
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510 </param>
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511 <param argument="--cmin" type="integer" value="2" optional="true" label="Specify minimum number of categories for FreeRate model"/>
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512 <param argument="--cmax" type="integer" value="10" optional="true" label="Specify maximum number of categories for FreeRate model"/>
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513 <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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514 <option value="AIC">AIC</option>
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515 <option value="AICc">AICc</option>
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516 <option value="BIC">BIC</option>
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517 </param>
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518 <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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519 <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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520 <expand macro="sanitize_query"
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521 validinitial="string.ascii_uppercase,string.digits,string.punctuation" />
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522 </param>
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523 <param argument="--mdef" type="data" format="txt" optional="true" label="Specify a NEXUS model file to define new models."/>
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524 <param argument="--modelomatic" type="boolean" truevalue="--modelomatic" falsevalue="" label="Find best codon/protein/DNA models" />
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525 </section>
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526 <section name="specifying_substitution" expanded="False" title="Specifying substitution models">
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527 <param argument="--mix-opt" type="boolean" truevalue="--mix-opt" 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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528 </section>
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529 <section name="rate_heterogeneity" expanded="False" title="Rate heterogeneity">
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530 <param argument="--alpha-min" type="text" optional="true" label="Specify the minimum Gamma shape parameter (default: estimate)">
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531 <expand macro="sanitize_query" />
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532 </param>
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533 <param argument="--gamma-median" type="boolean" truevalue="--gamma-median" falsevalue="" checked="false" label="Perform the median approximation for Gamma rate heterogeneity instead of the default mean approximation (Yang, 1994)"/>
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534 <param argument="-i" type="text" optional="true" label="Specify the proportion of invariable sites (default: estimate)">
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535 <expand macro="sanitize_query" />
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536 </param>
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537 <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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538 <param argument="--rate" type="boolean" truevalue="--rate" falsevalue="" checked="false" label="Write empirical Bayesian site rates to .rate file"/>
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539 <param argument="--mlrate" type="boolean" truevalue="--mlrate" falsevalue="" checked="false" label="Write maximum likelihood site rates to .mlrate file"/>
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540 </section>
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541 <section name="partition_model" expanded="False" title="Partition model options">
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542 <conditional name="model_selection">
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543 <param name="model" type="select" label="Partition model">
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544 <option value="none">No partition model</option>
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545 <option value="p">Edge-linked proportional partition model</option>
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546 <option value="q">Edge-linked equal partition model</option>
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547 <option value="Q">Edge-unlinked proportional partition model</option>
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548 <option value="S">Separate tree inference</option>
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549 </param>
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550 <when value="none" />
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551 <when value="p">
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552 <param argument="-p" name="model_file" type="data" format="nex" optional="true" label="Partition file" />
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553 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
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554 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
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555 </when>
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556 <when value="q">
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557 <param argument="-q" name="model_file" type="data" format="nex" optional="true" label="Partition file" />
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558 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
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559 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
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560 </when>
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561 <when value="Q">
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562 <param argument="-Q" name="model_file" type="data" format="nex" optional="true" label="Partition file" />
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563 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
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564 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
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565 </when>
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566 <when value="S">
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567 <param argument="-S" name="model_file" type="data" format="nex" optional="true" label="Partition file" />
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568 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
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569 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
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570 </when>
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571 </conditional>
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572 </section>
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573 <section name="site_specific_frequency" expanded="False" title="Site-specific frequency model options">
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574 <param argument="--tree-freq" type="data" format="nhx" optional="true" label="Specify a guide tree to infer site frequency profiles."/>
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575 <param argument="--site-freq" 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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576 <param argument="--freq-max" type="boolean" truevalue="--freq-max" falsevalue="" checked="false" label="Switch to posterior maximum mode for obtaining site-specific profiles" help="Default: posterior mean."/>
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577 </section>
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578 </section>
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579 <section name="tree_parameters" title="Tree Parameters">
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580 <section name="tree_search" expanded="False" title="Tree search parameters">
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581 <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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582 <param argument="--ninit" type="integer" value="100" optional="true" label="Specify number of initial parsimony trees"/>
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583 <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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584 <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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585 <param argument="--nstop" type="integer" value="100" optional="true" label="Specify number of unsuccessful iterations to stop"/>
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586 <param argument="--radius" type="integer" value="6" optional="true" label="Specify SPR radius for the initial parsimony tree search"/>
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587 <param argument="--perturb" type="float" value="0.5" optional="true" label="Specify perturbation strength (between 0 and 1) for randomized NNI"/>
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588 <param argument="--allnni" type="boolean" truevalue="-allnni" falsevalue="" checked="false" label="Turn on more thorough and slower NNI search"/>
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589 <param argument="--tree-fix" type="boolean" truevalue="--tree-fix" falsevalue="" checked="false" label="Avoid computing ML pairwise distances and BIONJ tree."/>
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590 <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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591 <param argument="--fast" type="boolean" truevalue="--fast" falsevalue="" label="Fast search to resemble FastTree" />
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592 <param argument="--polytomy" type="boolean" truevalue="--polytomy" falsevalue="" label="Collapse near-zero branches into polytomy" />
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593 <param argument="--treels" type="boolean" truevalue="--treels" falsevalue="" label="Write locally optimal trees into .treels file" />
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594 <param argument="--show-lh" type="boolean" truevalue="--show-lh" falsevalue="" label="Compute tree likelihood without optimisation" />
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595 <param argument="--terrace" type="boolean" truevalue="--terrace" falsevalue="" label="Check if the tree lies on a phylogenetic terrace" />
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596 </section>
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597 <section name="single_branch" expanded="False" title="Single branch tests">
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598 <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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599 <param argument="--abayes" type="boolean" truevalue="-abayes" falsevalue="" checked="false" label="Perform approximate Bayes test (Anisimova et al., 2011)."/>
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600 <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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601 </section>
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602 <section name="tree_topology" expanded="False" title="Tree topology tests">
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603 <param argument="--trees" 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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604 <param argument="--test" 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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605 <param argument="--test-weight" type="boolean" truevalue="--test-weight" falsevalue="" checked="false" label="Used together with --test to additionally perform the weighted-KH and weighted-SH tests."/>
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606 <param argument="--test-au" type="boolean" truevalue="--test-au" falsevalue="" checked="false" label="Used together with --test 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 -test."/>
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607 </section>
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608 <section name="constructing_consensus" expanded="False" title="Constructing consensus tree">
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609 <param argument="--contree" type="boolean" truevalue="--contree" 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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610 <param argument="--connet" type="boolean" truevalue="--connet" 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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611 <param argument="--sup-min" 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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612 <param argument="--burnin" 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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613 <param argument="--support" 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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614 <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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615 </section>
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616 <section name="computing_robinson_foulds" expanded="False" title="Computing Robinson-Foulds distance">
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617 <param argument="--tree-dist-all" type="boolean" truevalue="--tree-dist-all" falsevalue="" checked="false" label="Compute all-to-all RF distances between all trees passed via -t"/>
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618 <param argument="--tree-dist" type="data" format="nhx" optional="true" label="Compute RF distances between -t trees and this set" />
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619 <param argument="--tree-dist2" type="data" format="nhx" optional="true" label="Like -rf but trees can have unequal taxon sets" />
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620
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621 </section>
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622 <section name="generating_random" expanded="False" title="Generating random trees">
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623 <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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624 <param argument="--rand" type="select" optional="true" label="Random tree creation">
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625 <option value="--rand UNI">Uniform model</option>
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626 <option value="--rand CAT">Random caterpillar tree</option>
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627 <option value="--rand BAL">Random balanced tree</option>
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628 </param>
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629 <param name="branch_min" type="integer" optional="true" label="Minimum branch lengths of the random tree" />
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630 <param name="branch_mean" type="integer" optional="true" label="Median branch lengths of the random tree" />
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631 <param name="branch_max" type="integer" optional="true" label="Maximum branch lengths of the random tree" />
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632 </section>
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633 <section name="ancestral_state" title="Ancestral State Reconstruction">
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634 <param argument="--ancestral" type="boolean" truevalue="--ancestral" falsevalue="" label="Perform ancestral state reconstruction by empirical Bayes" />
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635 <param argument="--asr-min" type="float" optional="true" min="0" max="1" label="Minimum probability of ancestral state" />
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636 </section>
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637 <section name="symmetry_test" title="Symmetry Tests">
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638 <param argument="--symtest" type="boolean" truevalue="--symtest" falsevalue="" label="Perform three tests of symmetry" />
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639 <param argument="--symtest-remove-bad" type="boolean" truevalue="--symtest-remove-bad" falsevalue="" label="Do --symtest and remove bad partitions" />
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640 <param argument="--symtest-remove-good" type="boolean" truevalue="--symtest-remove-good" falsevalue="" label="Do --symtest and remove good partitions" />
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641 <param argument="--symtest-type" type="select" optional="true" label="Type of test to use">
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642 <option value="MAR">Marginal</option>
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643 <option value="INT">Internal</option>
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644 </param>
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645 <param argument="--symtest-pval" type="float" optional="true" label="P-value cutoff" />
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646 <param argument="--symtest-keep-zero" type="boolean" truevalue="--symtest-keep-zero" falsevalue="" label="Keep NAs in the tests" />
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647 </section>
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648 <section name="concordance_factor" title="Concordance Factor Analysis">
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649 <param argument="--gcf" type="data" format="nex" optional="true" label="Set of source trees for gene concordance factor" />
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650 <param argument="--df-tree" type="boolean" truevalue="--df-tree" falsevalue="" label="Write discordant trees associated with gDF1" />
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651 <param argument="--scf" type="integer" optional="true" label="Number of quartets for site concordance factor" />
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652 <param argument="--cf-verbose" type="boolean" truevalue="--cf-verbose" falsevalue="" label="Write CF per tree/locus" />
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653 <param argument="--cf-quartet" type="boolean" truevalue="--cf-quartet" falsevalue="" label="Write sCF for all resampled quartets to .cf.quartet" />
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654 </section>
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655 </section>
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656 <section name="bootstrap_parameters" title="Bootstrap Parameters">
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657 <section name="ultrafast_bootstrap" expanded="False" title="Ultrafast bootstrap parameters">
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658 <param argument="--ufboot" type="integer" optional="true" label="Specify number of bootstrap replicates (&gt;=1000)."/>
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659 <param argument="--ufjack" type="integer" optional="true" label="Specify number of replicates for ultrafast jackknife (&gt;=1000)."/>
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660 <param argument="--jack-prop" type="float" optional="true" min="0" max="1" label="Subsampling proportion for jackknife." help="Default: 0.5"/>
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661 <param argument="--boot-trees" type="boolean" truevalue="--boot-trees" falsevalue="" checked="false" label="Turn on writing bootstrap trees to .ufboot file"/>
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662 <param argument="--wbtl" type="boolean" truevalue="--wbtl" falsevalue="" checked="false" label="Like -boot-trees but bootstrap trees written with branch lengths"/>
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663 <param argument="--nmax" type="integer" value="1000" optional="true" label="Specify maximum number of iterations to stop"/>
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664 <param argument="--bcor" type="float" value="0.99" optional="true" label="Specify minimum correlation coefficient for UFBoot convergence criterion"/>
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665 <param argument="--nstep" type="integer" value="100" optional="true" label="Specify iteration interval checking for UFBoot convergence"/>
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666 <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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667 <param argument="--sampling" type="text" optional="true" label="Specify the resampling strategies for partitioned analysis" help="By default, IQ-TREE resamples alignment sites within partitions. With --sampling GENE IQ-TREE will resample partitions. With --sampling GENESITE IQ-TREE will resample partitions and then resample sites within resampled partitions (Gadagkar et al., 2005).">
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668 <sanitizer>
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669 <valid initial="string.ascii_uppercase" />
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670 </sanitizer>
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671 </param>
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672 <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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673 </section>
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674 <section name="nonparametric_bootstrap" expanded="False" title="Nonparametric bootstrap">
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675 <param argument="--boot" type="integer" optional="true" label="Replicates for bootstrap + ML tree + consensus tree" help="This will perform both bootstrap and analysis on original alignment and provide a consensus tree."/>
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676 <param argument="--jack" type="integer" optional="true" label="Replicates for jackknife + ML tree + consensus tree" help="This will perform both bootstrap and analysis on original alignment and provide a consensus tree."/>
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677 <param argument="--jack-prop" type="float" optional="true" min="0" max="1" label="Subsampling proportion for jackknife." help="Default: 0.5"/>
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678 <param argument="--bcon" type="integer" optional="true" label="Replicates for bootstrap + consensus tree"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
679 <param argument="--bonly" type="integer" optional="true" label="Replicates for bootstrap only"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
680 <param argument="--tbe" type="boolean" truevalue="--tbe" falsevalue="" checked="false" label="Transfer bootstrap expectation"/>
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
681 </section>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
682 </section>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
683 <section name="miscellaneous_options" expanded="False" title="Miscellaneous options">
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
684 <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.">
2
d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
685 <expand macro="sanitize_query"
d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
686 validinitial="string.digits,string.punctuation" />
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
687 </param>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
688 </section>
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
689 </inputs>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
690 <outputs>
4
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
691 <data name="bionj" format="nhx" from_work_dir="*.bionj" label="${tool.name} on ${on_string}: BIONJ Tree" />
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
692 <data name="treefile" format="nhx" from_work_dir="*.treefile" label="${tool.name} on ${on_string}: MaxLikelihood Tree" />
11
563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
693 <data name="consensus_tree" format="nhx" from_work_dir="*.contree" label="${tool.name} on ${on_string}: Consensus Tree">
563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
694 <filter>tree_parameters['constructing_consensus']['contree']</filter>
563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
695 </data>
4
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
696 <data name="mldist" format="mldist" from_work_dir="*.mldist" label="${tool.name} on ${on_string}: MaxLikelihood Distance Matrix"/>
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
697 <data name="splits" format="nex" from_work_dir="*.splits.nex" label="${tool.name} on ${on_string}: Occurence Frequencies in Bootstrap Trees" />
4
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
698 <data name="iqtree" format="iqtree" from_work_dir="*.iqtree" label="${tool.name} on ${on_string}: Report and Final Tree" />
7
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
699 <data name="mlrate" format="data" from_work_dir="*.mlrate" label="${tool.name} on ${on_string}: ML Rates">
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
700 <filter>modelling_parameters['rate_heterogeneity']['mlrate']</filter>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
701 </data>
7
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
702 <data name="timetree" format="nex" from_work_dir="PREF.timetree.nex" label="${tool.name} on ${on_string}: Tree labeled with dates">
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
703 <filter>time_tree['date_source']['select_source'] != 'none'</filter>
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
704 </data>
9
f58a10e2e46d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 00ddca12cd441fab5c928f93c62fa8aa79160967"
iuc
parents: 8
diff changeset
705 <data name="lsd_report" format="txt" from_work_dir="PREF.timetree.lsd" label="${tool.name} on ${on_string}: LSD Report">
f58a10e2e46d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 00ddca12cd441fab5c928f93c62fa8aa79160967"
iuc
parents: 8
diff changeset
706 <filter>time_tree['date_source']['select_source'] != 'none'</filter>
f58a10e2e46d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 00ddca12cd441fab5c928f93c62fa8aa79160967"
iuc
parents: 8
diff changeset
707 </data>
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
708 </outputs>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
709 <tests>
11
563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
710 <test expect_num_outputs="5">
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
711 <param name="seed" value="1257" />
12
9b892d7f82cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3b1c44e42b042ccbbe2d9e01c77d18f109d4984f"
iuc
parents: 11
diff changeset
712 <param name="seqtype" value="DNA" />
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
713 <param name="s" value="example.phy" />
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
714 <param name="m" value="TEST" />
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
715 <param name="msub" value="nuclear" />
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
716 <param name="madd" value="LG4M,LG4X" />
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
717 <param name="merit" value="AICc" />
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
718 <param name="ufboot" value="1000" />
4
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
719 <output name="bionj">
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
720 <assert_contents>
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
721 <has_text_matching expression=".*Whale.*" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
722 <has_text_matching expression=".*Human.*" />
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
723 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
724 </output>
4
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
725 <output name="iqtree">
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
726 <assert_contents>
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
727 <has_text_matching expression="GTR\+F(\s+((-|\d|\.)+))+" />
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
728 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
729 </output>
4
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
730 <output name="mldist">
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
731 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
732 <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
733 <has_line_matching expression="^Whale(\s+((\d|\.)+))+\s+$" />
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
734 <has_line_matching expression="^Cow(\s+((\d|\.)+))+\s+$" />
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
735 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
736 </output>
4
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
737 <output name="treefile">
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
738 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
739 <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
740 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
741 </output>
11
563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
742 <output name="consensus_tree">
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
743 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
744 <has_line_matching
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
745 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
746 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
747 </output>
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
748 <output name="splits">
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
749 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
750 <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
751 <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
752 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
753 </output>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
754 </test>
11
563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
755 <test expect_num_outputs="5">
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
756 <!-- 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
757 <param name="seed" value="1257" />
12
9b892d7f82cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3b1c44e42b042ccbbe2d9e01c77d18f109d4984f"
iuc
parents: 11
diff changeset
758 <param name="seqtype" value="DNA" />
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
759 <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
760 <!-- <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
761 <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
762 <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
763 <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
764 <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
765 <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
766 <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
767 <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
768 <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
769 <param name="nstop" value="100" />
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
770 <param name="radius" value="6" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
771 <param name="perturb" value="0.5" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
772 <param name="sup_min" value="0.0" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
773 <param name="nmax" value="1000" />
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
774 <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
775 <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
776 <param name="beps" value="0.5" />
4
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
777 <output name="iqtree">
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
778 <assert_contents>
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
779 <has_text_matching expression="GTR\+F\+I(\s+((-|\d|\.)+))+" />
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
780 </assert_contents>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
781 </output>
4
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
782 <output name="treefile">
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
783 <assert_contents>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
784 <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
785 </assert_contents>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
786 </output>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
787 </test>
11
563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
788 <test expect_num_outputs="5">
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
789 <!-- 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
790 <param name="seed" value="1257" />
12
9b892d7f82cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3b1c44e42b042ccbbe2d9e01c77d18f109d4984f"
iuc
parents: 11
diff changeset
791 <param name="seqtype" value="DNA" />
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
792 <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
793 <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
794 <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
795 <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
796 <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
797 <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
798 <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
799 <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
800 <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
801 <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
802 <param name="nstop" value="100" />
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
803 <param name="radius" value="6" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
804 <param name="perturb" value="0.5" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
805 <param name="sup_min" value="0.0" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
806 <param name="nmax" value="1000" />
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
807 <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
808 <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
809 <param name="beps" value="0.5" />
4
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
810 <output name="iqtree">
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
811 <assert_contents>
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
812 <has_text_matching expression="GTR\+F\+I\+G4(\s+((-|\d|\.)+))+" />
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
813 </assert_contents>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
814 </output>
4
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
815 <output name="treefile">
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
816 <assert_contents>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
817 <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
818 </assert_contents>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
819 </output>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
820 </test>
11
563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
821 <test expect_num_outputs="5">
4
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
822 <param name="s" value="example.phy" />
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
823 <output name="iqtree">
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
824 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
825 <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
826 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
827 </output>
4
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
828 <output name="treefile">
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
829 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
830 <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
831 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
832 </output>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
833 </test>
11
563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
834 <test expect_num_outputs="5">
4
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
835 <param name="s" value="example.phy" />
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
836 <param name="opt_custommodel" value="true" />
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
837 <param name="m" value="GTR+G{0.9}" />
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
838 <output name="iqtree">
3
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
839 <assert_contents>
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
840 <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
841 </assert_contents>
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
842 </output>
4
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
843 <output name="treefile">
3
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
844 <assert_contents>
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
845 <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
846 </assert_contents>
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
847 </output>
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
848 </test>
11
563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
849 <test expect_num_outputs="5">
4
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
850 <param name="s" value="short.fasta" />
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
851 <param name="short_alignments" value="true" />
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
852 <output name="treefile">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
853 <assert_contents>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
854 <has_line_matching expression="\(NC_045512.+\(MT019531.+MT019532.+" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
855 </assert_contents>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
856 </output>
4
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
857 </test>
11
563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
858 <test expect_num_outputs="7">
7
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
859 <param name="s" value="dates.fa" />
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
860 <param name="n" value="100" />
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
861 <param name="seed" value="122125" />
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
862 <param name="select_source" value="dataset" />
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
863 <param name="date" value="dates.tabular" />
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
864 <output name="timetree">
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
865 <assert_contents>
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
866 <has_line_matching expression=".+222-3pu_03-28-01_985737600.+" />
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
867 </assert_contents>
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
868 </output>
9
f58a10e2e46d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 00ddca12cd441fab5c928f93c62fa8aa79160967"
iuc
parents: 8
diff changeset
869 <output name="lsd_report">
f58a10e2e46d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 00ddca12cd441fab5c928f93c62fa8aa79160967"
iuc
parents: 8
diff changeset
870 <assert_contents>
f58a10e2e46d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 00ddca12cd441fab5c928f93c62fa8aa79160967"
iuc
parents: 8
diff changeset
871 <has_line_matching expression="^LEAST-SQUARE METHODS.+" />
f58a10e2e46d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 00ddca12cd441fab5c928f93c62fa8aa79160967"
iuc
parents: 8
diff changeset
872 </assert_contents>
f58a10e2e46d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 00ddca12cd441fab5c928f93c62fa8aa79160967"
iuc
parents: 8
diff changeset
873 </output>
7
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
874 </test>
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
875 </tests>
2
d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
876 <help><![CDATA[
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
877 IQ-TREE
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
878 =======
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 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
881
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
882 .. _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
883
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
884 General Tutorial
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
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
887 Input data
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
888 ----------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
889
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
890 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
891
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
892 .. _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
893
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
894 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
895
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
896 7 28
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
897 Frog AAATTTGGTCCTGTGATTCAGCAGTGAT
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
898 Turtle CTTCCACACCCCAGGACTCAGCAGTGAT
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
899 Bird CTACCACACCCCAGGACTCAGCAGTAAT
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
900 Human CTACCACACCCCAGGAAACAGCAGTGAT
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
901 Cow CTACCACACCCCAGGAAACAGCAGTGAC
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
902 Whale CTACCACGCCCCAGGACACAGCAGTGAT
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
903 Mouse CTACCACACCCCAGGACTCAGCAGTGAT
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
904
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
905 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
906
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
907 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
908
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
909 >Frog
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
910 AAATTTGGTCCTGTGATTCAGCAGTGAT
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
911 >Turtle
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
912 CTTCCACACCCCAGGACTCAGCAGTGAT
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
913 >Bird
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
914 CTACCACACCCCAGGACTCAGCAGTAAT
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
915 >Human
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
916 CTACCACACCCCAGGAAACAGCAGTGAT
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
917 >Cow
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
918 CTACCACACCCCAGGAAACAGCAGTGAC
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
919 >Whale
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
920 CTACCACGCCCCAGGACACAGCAGTGAT
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
921 >Mouse
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
922 CTACCACACCCCAGGACTCAGCAGTGAT
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
923
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
924 **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
925
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
926 .. _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
927 .. _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
928
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
929
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
930 Running example
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
931 ---------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
932
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
933 From the download_ there is an example alignment called `example.phy`
13
24d024316465 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 25f53344278285ac5e75ac902aec60a38921aa12
iuc
parents: 12
diff changeset
934 in PHYLIP format. This example contains parts of the mitochondrial DNA sequences of several animals.
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
935
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
936 .. _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
937
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
938 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
939 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
940
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
941 ::iqtree -s example.phy -st AA -seed 9999 -m TESTNEW -msub nuclear -madd LG4M,LG4x -merit AICc --ufboot 2000
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
942
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
943 * **-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
944
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
945 * **-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
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diff changeset
946
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
947 * **-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
948
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
949 * **-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
950
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
951 * **-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
952
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
953 * **-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
954
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
955 * **-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
956
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
957 * **-ufboot** 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
958
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
959
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
960 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
961
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
962 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
963
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
964 * **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
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diff changeset
965
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
966 * **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
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diff changeset
967
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
968 **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
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diff changeset
969
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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970 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
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diff changeset
971
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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972 **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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973
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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974 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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975
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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976 +--------------LngfishAu
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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977 |
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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978 | +--------------LngfishSA
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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979 +--------|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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980 | +--------------LngfishAf
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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981 |
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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982 | +-------------------Frog
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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983 +------|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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984 | +-----------------Turtle
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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985 | +-----|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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986 | | | +-----------------------Sphenodon
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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987 | | | +--|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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988 | | | | +--------------------------Lizard
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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989 | | +---|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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990 | | | +---------------------Crocodile
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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991 | | +------|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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992 | | +------------------Bird
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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993 +---------|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
994 | +----------------Human
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
995 | +--|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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996 | | | +--------Seal
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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997 | | +--|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
998 | | | +-------Cow
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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999 | | +---|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1000 | | +---------Whale
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
1001 | +----|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
1002 | | | +------Mouse
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1003 | | +---------|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
1004 | | +--------Rat
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
1005 +----------|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1006 | +----------------Platypus
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
1007 +---|
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
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diff changeset
1008 +-------------Opossum
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1009
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
1010
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
1011 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
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1012
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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parents:
diff changeset
1013 Choosing the right substitution model
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1014 -------------------------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1015
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
1016 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
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1017
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1018 .. _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
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1019
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1020
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1021 ------------------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1022
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1023 Advanced Parameter Selection
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1024 ============================
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1025
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1026 Using codon models
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1027 ------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1028
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1029 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
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1030
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1031 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1032
1
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diff changeset
1033 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
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1034
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1035 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
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1036
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1037 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
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1038
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1039 ::
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
1040
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
1041 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
1042
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1043 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
1044
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1045
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1046 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
1047 ----------------------------------------------------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1048
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1049 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
1050
1
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
1051 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
1052
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1053 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1054
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
1055 iqtree -s example.phy -m TIM2+I+G --ufboot 1000
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1056
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
1057 **-ufboot** 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:
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1058
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1059 * **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
1060
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1061 * **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
1062
13
24d024316465 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 25f53344278285ac5e75ac902aec60a38921aa12
iuc
parents: 12
diff changeset
1063 * **example.phy.splits.nex**: has the same information as **example.phy.splits** but in NEXUS format, which can be viewed with the program IcyTree_ 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.
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1064
13
24d024316465 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 25f53344278285ac5e75ac902aec60a38921aa12
iuc
parents: 12
diff changeset
1065 .. _IcyTree: https://icytree.org
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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parents:
diff changeset
1066
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1067
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1068 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
1069 ------------------------------------------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1070
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1071 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
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diff changeset
1072
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1073 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
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diff changeset
1074
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
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parents: 4
diff changeset
1075 iqtree -s example.phy -m TIM2+I+G --ufboot 1000 -bnni
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
1076
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1077 For more details see:
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
1078
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
1079 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
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diff changeset
1080
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1081
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1082 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
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diff changeset
1083 ----------------------------------------------------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1084
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1085 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
1086
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1087 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
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parents:
diff changeset
1088
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1089 **-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
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diff changeset
1090 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
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diff changeset
1091
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1092
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1093
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1094 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
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diff changeset
1095 --------------------------------------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
1096
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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diff changeset
1097 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
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diff changeset
1098
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
1099 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
1100
5
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diff changeset
1101 iqtree -s example.phy -m TIM2+I+G --alrt 1000
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1102
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
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diff changeset
1103 **--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
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diff changeset
1104
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1105 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
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diff changeset
1106
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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parents:
diff changeset
1107 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
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diff changeset
1108
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
1109 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
1110
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
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diff changeset
1111 iqtree -s example.phy -m TIM2+I+G --alrt 1000 --ufboot 1000
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
1112
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
1113 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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diff changeset
1114
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1115 **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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diff changeset
1116 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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1117
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1118 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1119
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diff changeset
1120 +-------------LngfishAu
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
1121 |
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1122 | +--------------LngfishSA
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1123 +-------| (100/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1124 | +------------LngfishAf
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1125 |
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1126 | +--------------------Frog
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1127 +------| (99.8/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1128 | +-----------------Turtle
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1129 | +--| (85/72)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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diff changeset
1130 | | | +------------------------Crocodile
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
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1131 | | +----| (96.5/97)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1132 | | +------------------Bird
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1133 | +--| (39/51)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1134 | | +---------------------------Sphenodon
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1135 | +-----| (98.2/99)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1136 | | +-------------------------------Lizard
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1137 +---------| (100/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1138 | +--------------Human
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1139 | +--| (92.3/93)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1140 | | | +------Seal
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1141 | | +--| (68.3/75)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1142 | | | +-----Cow
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1143 | | +--| (99.7/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1144 | | +-------Whale
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1145 | +----| (99.1/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1146 | | | +---Mouse
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1147 | | +---------| (100/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1148 | | +------Rat
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1149 +-----------| (100/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1150 | +--------------Platypus
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1151 +--| (93/98)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1152 +-----------Opossum
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1153
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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1154
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1155 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
d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
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parents: 1
diff changeset
1156 ]]></help>
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1157 <citations>
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
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parents: 4
diff changeset
1158 <citation type="doi">10.1038/nmeth.4285</citation>
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
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1159 <citation type="doi">10.1093/molbev/msu300</citation>
5
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
1160 <citation type="doi">10.1093/molbev/msx281</citation>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
1161 <citation type="doi">10.1093/sysbio/syx068</citation>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
1162 <citation type="doi">10.1093/sysbio/syw037</citation>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
1163 <citation type="doi">10.1016/j.jtbi.2016.07.042</citation>
0
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1164 <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
iuc
parents:
diff changeset
1165 </citations>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
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1166 </tool>